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PanDDA analysis group deposition -- Endothiapepsin changed state model for fragment F2X-Entry Library D11b
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 35.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.24 α = 90 b = 73.245 β = 109.14 c = 52.59 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 1.1 28.17 96.8 0.064 0.07 0.999 10.96 6.342 121886 14.958
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 0.97 1.03 0.824 2.078 2.363 0.263 0.53 3.62 31079
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 1.1 28.17 121886 6529 99.09 0.1489 0.14835 0.1497 0.14889 0.1482 RANDOM 12.961
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] -0.17 -0.38 0.06 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.222 r_dihedral_angle_4_deg 17.43 r_dihedral_angle_1_deg 11.454 r_dihedral_angle_3_deg 10.844 r_angle_refined_deg 2.121 r_angle_other_deg 1.739 r_mcangle_it 1.597 r_mcbond_it 1.095 r_mcbond_other 1.089 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.222 r_dihedral_angle_4_deg 17.43 r_dihedral_angle_1_deg 11.454 r_dihedral_angle_3_deg 10.844 r_angle_refined_deg 2.121 r_angle_other_deg 1.739 r_mcangle_it 1.597 r_mcbond_it 1.095 r_mcbond_other 1.089 r_chiral_restr 0.107 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 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 335 Heterogen Atoms 90
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing PHENIX refinement