5RCB

PanDDA analysis group deposition -- Endothiapepsin changed state model for fragment F2X-Entry Library G09a


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62900.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
1.935.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.204α = 90
b = 73.125β = 109.32
c = 52.644γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-03-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.827MAX IVBioMAX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
10.9942.6997.80.0530.0570.99913.36.55816743915.171
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.991.050.871.5611.7310.3370.844.6129062

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT0.9942.69167439898497.850.15880.158390.15876RANDOM12.578
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]
-0.08-0.310.130.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.016
r_dihedral_angle_4_deg16.714
r_dihedral_angle_1_deg11.648
r_dihedral_angle_3_deg11.261
r_angle_refined_deg2.56
r_angle_other_deg1.668
r_mcangle_it1.483
r_mcbond_it1.007
r_mcbond_other0.991
r_chiral_restr0.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.016
r_dihedral_angle_4_deg16.714
r_dihedral_angle_1_deg11.648
r_dihedral_angle_3_deg11.261
r_angle_refined_deg2.56
r_angle_other_deg1.668
r_mcangle_it1.483
r_mcbond_it1.007
r_mcbond_other0.991
r_chiral_restr0.089
r_bond_refined_d0.025
r_gen_planes_refined0.009
r_gen_planes_other0.004
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2371
Nucleic Acid Atoms
Solvent Atoms254
Heterogen Atoms104

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing
PHENIXrefinement