5RD3

PanDDA analysis group deposition -- Endothiapepsin ground state model 25


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
1.8834.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.233α = 90
b = 72.925β = 109.23
c = 52.378γ = 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
10.9342.7488.20.0620.0670.99813.246.59418031513.497
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)
10.930.990.5171.5281.7150.320.772.4834830

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 SYNTHESISTHROUGHOUT0.9342.74180315965588.260.1520.151710.15199RANDOM11.584
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]
-0.31-0.290.110.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.253
r_dihedral_angle_4_deg17.595
r_dihedral_angle_3_deg8.476
r_dihedral_angle_1_deg6.87
r_angle_refined_deg1.939
r_angle_other_deg1.64
r_mcangle_it1.487
r_mcbond_it1.056
r_mcbond_other1.054
r_chiral_restr0.108
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.253
r_dihedral_angle_4_deg17.595
r_dihedral_angle_3_deg8.476
r_dihedral_angle_1_deg6.87
r_angle_refined_deg1.939
r_angle_other_deg1.64
r_mcangle_it1.487
r_mcbond_it1.056
r_mcbond_other1.054
r_chiral_restr0.108
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2369
Nucleic Acid Atoms
Solvent Atoms341
Heterogen Atoms63

Software

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