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PanDDA analysis group deposition -- Endothiapepsin ground state model 51
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 1.88 34.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.1 α = 90 b = 73.18 β = 108.98 c = 52.188 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 1.05 49.4 99.1 0.097 0.105 0.998 9.44 6.6 138840 15.108
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 1.05 1.12 0.956 1.575 1.719 0.404 0.82 6.15 23781
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 1.05 49.4 138840 7266 99.16 0.2036 0.20263 0.204 0.20359 0.2008 RANDOM 11.736
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 -0.33 -0.14 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.496 r_dihedral_angle_4_deg 17.893 r_dihedral_angle_3_deg 8.968 r_dihedral_angle_1_deg 6.932 r_angle_refined_deg 1.884 r_angle_other_deg 1.671 r_mcangle_it 1.664 r_mcbond_it 1.139 r_mcbond_other 1.136 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.496 r_dihedral_angle_4_deg 17.893 r_dihedral_angle_3_deg 8.968 r_dihedral_angle_1_deg 6.932 r_angle_refined_deg 1.884 r_angle_other_deg 1.671 r_mcangle_it 1.664 r_mcbond_it 1.139 r_mcbond_other 1.136 r_chiral_restr 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2369 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing PHENIX refinement