X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5XA3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE277PEG 8000, Magnesium Chloride, Tris-HCl, 0.5% DMSO, 200 uM N-Enanthyl-L-Prolyl-L-Phenylalanine
Crystal Properties
Matthews coefficientSolvent content
2.6854.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.055α = 90
b = 126.769β = 90
c = 149γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-05-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.99999SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.4148.321000.0650.0670.018117.113.4215305
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.411.4399.92.2272.3370.7020.687110.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5XA31.4148.322044851070299.950.14630.14470.1776RANDOM22.196
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]
-0.20.190.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.056
r_dihedral_angle_4_deg16.09
r_dihedral_angle_3_deg12.644
r_dihedral_angle_1_deg6.552
r_rigid_bond_restr2.282
r_angle_refined_deg1.629
r_angle_other_deg1.486
r_chiral_restr0.092
r_bond_refined_d0.01
r_gen_planes_refined0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.056
r_dihedral_angle_4_deg16.09
r_dihedral_angle_3_deg12.644
r_dihedral_angle_1_deg6.552
r_rigid_bond_restr2.282
r_angle_refined_deg1.629
r_angle_other_deg1.486
r_chiral_restr0.092
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7335
Nucleic Acid Atoms
Solvent Atoms877
Heterogen Atoms340

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction