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PanDDA analysis group deposition -- Endothiapepsin changed state model for fragment F2X-Entry Library E06a
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 290 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.9 35.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.221 α = 90 b = 73.236 β = 109.01 c = 52.403 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2019-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.827 MAX IV BioMAX
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.03 42.79 93.1 0.086 0.094 0.998 8.98 6.829 147538 17.807
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) Redundancy Number Unique Reflections (All) 1 1.04 1.1 0.801 2.32 2.505 0.334 0.62 5.42 24993
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.03 42.79 147538 7730 98.43 0.162 0.16142 0.1694 0.16199 0.1689 RANDOM 14.596
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 -0.2 0.12 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.517 r_dihedral_angle_4_deg 18.782 r_dihedral_angle_3_deg 9.086 r_dihedral_angle_1_deg 6.629 r_angle_refined_deg 1.862 r_mcangle_it 1.696 r_angle_other_deg 1.624 r_mcbond_it 1.149 r_mcbond_other 1.149 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.517 r_dihedral_angle_4_deg 18.782 r_dihedral_angle_3_deg 9.086 r_dihedral_angle_1_deg 6.629 r_angle_refined_deg 1.862 r_mcangle_it 1.696 r_angle_other_deg 1.624 r_mcbond_it 1.149 r_mcbond_other 1.149 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2371 Nucleic Acid Atoms Solvent Atoms 325 Heterogen Atoms 104
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing PHENIX refinement