DtpAa Y389F 24 fs 10 microjoules XFEL Pulse Data Collection
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 6I43 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | | 298 | 12% v/v PEG 3350, 100 mM HEPES pH 7.0 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.21 | 44.44 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 72.72 | α = 90 |
| b = 68.2 | β = 105.6 |
| c = 74.6 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 1 21 1 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 294.15 | PIXEL | PSI JUNGFRAU 8M | | 2023-09-06 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | SwissFEL ARAMIS BEAMLINE ESA | 1.03 | SwissFEL ARAMIS | ESA |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | fixed target |
| Measurement |
|---|
| Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
|---|
| 1 | 22 (fs) | | | 12.03 (KeV) | |
Data Collection
| Overall |
|---|
| 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 |
|---|
| 1 | 1.33 | 35.05 | 100 | 0.971 | 5.89 | 247 | | 160910 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.34 | 1.37 | 100 | | 0.36 | 2.22 | 159.3 | |
Refinement
| Statistics |
|---|
| 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 |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.33 | 35.05 | 152910 | 7961 | 99.98 | 0.15403 | 0.15325 | 0.1535 | 0.16937 | 0.1694 | RANDOM | 18.339 |
| Temperature Factor Modeling |
|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
|---|
| 0.23 | | -0.03 | -0.32 | | 0.1 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_3_deg | 12.628 |
| r_dihedral_angle_2_deg | 10.484 |
| r_dihedral_angle_1_deg | 6.302 |
| r_long_range_B_refined | 5.952 |
| r_long_range_B_other | 5.909 |
| r_scangle_other | 4.946 |
| r_scbond_other | 3.208 |
| r_scbond_it | 3.207 |
| r_mcangle_other | 2.492 |
| r_mcangle_it | 2.489 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_3_deg | 12.628 |
| r_dihedral_angle_2_deg | 10.484 |
| r_dihedral_angle_1_deg | 6.302 |
| r_long_range_B_refined | 5.952 |
| r_long_range_B_other | 5.909 |
| r_scangle_other | 4.946 |
| r_scbond_other | 3.208 |
| r_scbond_it | 3.207 |
| r_mcangle_other | 2.492 |
| r_mcangle_it | 2.489 |
| r_angle_refined_deg | 1.88 |
| r_mcbond_it | 1.708 |
| r_mcbond_other | 1.705 |
| r_angle_other_deg | 0.644 |
| r_chiral_restr | 0.095 |
| r_bond_refined_d | 0.012 |
| r_gen_planes_refined | 0.01 |
| 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 |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 5548 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 532 |
| Heterogen Atoms | 86 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| REFMAC | refinement |
| CrystFEL | data scaling |
| REFMAC | phasing |
| Coot | model building |
| CrystFEL | data reduction |