5RC2

PanDDA analysis group deposition -- Endothiapepsin changed state model for fragment F2X-Entry Library E11b


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
1.8935.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.23α = 90
b = 73.009β = 108.95
c = 52.512γ = 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
10.9742.8297.40.0570.0610.99913.066.39217653714.56
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)
10.971.030.8521.7251.9570.3080.713.830833

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 SYNTHESISTHROUGHOUT0.9742.82176537948597.560.15410.153660.15408RANDOM12.188
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]
-0.14-0.19-0.090.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.547
r_dihedral_angle_4_deg16.016
r_dihedral_angle_3_deg10.844
r_dihedral_angle_1_deg6.622
r_angle_refined_deg2.257
r_angle_other_deg1.631
r_mcangle_it1.5
r_mcbond_it1.044
r_mcbond_other1.041
r_chiral_restr0.139
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.547
r_dihedral_angle_4_deg16.016
r_dihedral_angle_3_deg10.844
r_dihedral_angle_1_deg6.622
r_angle_refined_deg2.257
r_angle_other_deg1.631
r_mcangle_it1.5
r_mcbond_it1.044
r_mcbond_other1.041
r_chiral_restr0.139
r_bond_refined_d0.017
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2369
Nucleic Acid Atoms
Solvent Atoms294
Heterogen Atoms74

Software

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