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PanDDA analysis group deposition -- Endothiapepsin changed state model for fragment F2X-Entry Library F08b
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 1.89 35.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.218 α = 90 b = 73.077 β = 109.12 c = 52.517 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 1.18 42.76 99.4 0.076 0.083 0.999 12.39 6.751 100615 17.395
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 1.18 1.25 0.971 0.929 1.011 0.732 1.8 6.38 17228
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 1.18 42.76 100615 5423 99.42 0.1643 0.16376 0.1641 0.16432 0.1671 RANDOM 13.121
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] -0.46 0.07 -0.39 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.223 r_dihedral_angle_4_deg 17.199 r_dihedral_angle_3_deg 11.266 r_dihedral_angle_1_deg 6.69 r_angle_refined_deg 1.751 r_mcangle_it 1.615 r_angle_other_deg 1.606 r_mcbond_it 1.084 r_mcbond_other 1.08 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.223 r_dihedral_angle_4_deg 17.199 r_dihedral_angle_3_deg 11.266 r_dihedral_angle_1_deg 6.69 r_angle_refined_deg 1.751 r_mcangle_it 1.615 r_angle_other_deg 1.606 r_mcbond_it 1.084 r_mcbond_other 1.08 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2371 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 71
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing PHENIX refinement