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PanDDA analysis group deposition -- Endothiapepsin ground state model 02
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 1.93 36.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.637 α = 90 b = 73.348 β = 109.55 c = 52.977 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 1.22 49.97 87.8 0.104 0.114 0.999 10.1 6.475 90637 23.091
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 0.249 3.39 3.735 0.228 0.46 1.26 17567
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.22 49.97 90637 4724 98.26 0.1773 0.17642 0.17733 0.2003 RANDOM 13.298
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] -0.21 -0.36 0.29 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.818 r_dihedral_angle_4_deg 17.727 r_dihedral_angle_3_deg 9.681 r_dihedral_angle_1_deg 6.896 r_angle_refined_deg 1.806 r_mcangle_it 1.617 r_angle_other_deg 1.561 r_mcbond_it 1.134 r_mcbond_other 1.132 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.818 r_dihedral_angle_4_deg 17.727 r_dihedral_angle_3_deg 9.681 r_dihedral_angle_1_deg 6.896 r_angle_refined_deg 1.806 r_mcangle_it 1.617 r_angle_other_deg 1.561 r_mcbond_it 1.134 r_mcbond_other 1.132 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2369 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing PHENIX refinement