DtpAa Y389F 24 fs 100 microjoules XFEL Pulse Data Collection
Serial Crystallography (SX)
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 6I43 | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | BATCH MODE | | 298 | 12% v/v PEG 3350, 100 mM HEPES pH 7.0 |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.21 | 44.44 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 72.72 | α = 90 |
b = 68.2 | β = 105.6 |
c = 74.6 | γ = 90 |
Symmetry |
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Space Group | P 1 21 1 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 294.15 | PIXEL | PSI JUNGFRAU 8M | | 2023-09-05 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | FREE ELECTRON LASER | SwissFEL ARAMIS BEAMLINE ESA | 1.03 | SwissFEL ARAMIS | ESA |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | | fixed target |
Measurement |
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Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
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1 | 22 (fs) | | | undefined (KeV) | |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot |
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1 | 1.3 | 35.05 | 100 | 0.974 | 6.61 | 523 | | 172313 | | | |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 1.3 | 1.33 | 100 | | 0.36 | 1.75 | 326.7 | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.3 | 35.05 | 163665 | 8593 | 99.98 | 0.16144 | 0.16056 | 0.1663 | 0.17833 | 0.1837 | RANDOM | 17.228 |
Temperature Factor Modeling |
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
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0.21 | | 0.03 | -0.24 | | 0.01 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_3_deg | 12.047 |
r_dihedral_angle_2_deg | 8.593 |
r_dihedral_angle_1_deg | 6.413 |
r_long_range_B_refined | 5.495 |
r_long_range_B_other | 5.429 |
r_scangle_other | 4.406 |
r_scbond_other | 2.893 |
r_scbond_it | 2.892 |
r_mcangle_other | 2.319 |
r_mcangle_it | 2.318 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_3_deg | 12.047 |
r_dihedral_angle_2_deg | 8.593 |
r_dihedral_angle_1_deg | 6.413 |
r_long_range_B_refined | 5.495 |
r_long_range_B_other | 5.429 |
r_scangle_other | 4.406 |
r_scbond_other | 2.893 |
r_scbond_it | 2.892 |
r_mcangle_other | 2.319 |
r_mcangle_it | 2.318 |
r_angle_refined_deg | 1.84 |
r_mcbond_it | 1.584 |
r_mcbond_other | 1.582 |
r_angle_other_deg | 0.62 |
r_chiral_restr | 0.094 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.009 |
r_gen_planes_other | 0.005 |
r_bond_other_d | 0.001 |
r_dihedral_angle_4_deg | |
r_nbd_refined | |
r_nbd_other | |
r_nbtor_refined | |
r_nbtor_other | |
r_xyhbond_nbd_refined | |
r_xyhbond_nbd_other | |
r_metal_ion_refined | |
r_metal_ion_other | |
r_symmetry_vdw_refined | |
r_symmetry_vdw_other | |
r_symmetry_hbond_refined | |
r_symmetry_hbond_other | |
r_symmetry_metal_ion_refined | |
r_symmetry_metal_ion_other | |
r_scangle_it | |
r_rigid_bond_restr | |
r_sphericity_free | |
r_sphericity_bonded | |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 5544 |
Nucleic Acid Atoms | |
Solvent Atoms | 557 |
Heterogen Atoms | 86 |
Software
Software |
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Software Name | Purpose |
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REFMAC | refinement |
CrystFEL | data scaling |
CrystFEL | data reduction |
Coot | model building |
REFMAC | phasing |