9EPK | pdb_00009epk

DtpAa Y389F 24 fs 100 microjoules XFEL Pulse Data Collection


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6I43 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE29812% v/v PEG 3350, 100 mM HEPES pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.2144.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.72α = 90
b = 68.2β = 105.6
c = 74.6γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray294.15PIXELPSI JUNGFRAU 8M2023-09-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSwissFEL ARAMIS BEAMLINE ESA1.03SwissFEL ARAMISESA

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed target
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
122 (fs)undefined (KeV)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.335.051000.9746.61523172313
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.331000.361.75326.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.335.05163665859399.980.161440.160560.16630.178330.1837RANDOM17.228
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]
0.210.03-0.240.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.047
r_dihedral_angle_2_deg8.593
r_dihedral_angle_1_deg6.413
r_long_range_B_refined5.495
r_long_range_B_other5.429
r_scangle_other4.406
r_scbond_other2.893
r_scbond_it2.892
r_mcangle_other2.319
r_mcangle_it2.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.047
r_dihedral_angle_2_deg8.593
r_dihedral_angle_1_deg6.413
r_long_range_B_refined5.495
r_long_range_B_other5.429
r_scangle_other4.406
r_scbond_other2.893
r_scbond_it2.892
r_mcangle_other2.319
r_mcangle_it2.318
r_angle_refined_deg1.84
r_mcbond_it1.584
r_mcbond_other1.582
r_angle_other_deg0.62
r_chiral_restr0.094
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_gen_planes_other0.005
r_bond_other_d0.001
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 AtomsNumber
Protein Atoms5544
Nucleic Acid Atoms
Solvent Atoms557
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata scaling
CrystFELdata reduction
Cootmodel building
REFMACphasing