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PanDDA analysis group deposition -- Endothiapepsin ground state model 01
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 35.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.409 α = 90 b = 72.794 β = 109.4 c = 52.736 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 1.06 42.87 98.2 0.07 0.076 0.998 10.63 6.512 138960 17.919
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 0.908 1.813 1.974 0.457 0.81 5.83 24126
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 1.06 42.87 138960 7460 99.48 0.1699 0.16952 0.1733 0.1699 0.1712 RANDOM 13.28
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] 0.01 -0.37 0.17 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.883 r_dihedral_angle_4_deg 17.414 r_dihedral_angle_3_deg 8.941 r_dihedral_angle_1_deg 6.87 r_angle_refined_deg 1.953 r_mcangle_it 1.665 r_angle_other_deg 1.62 r_mcbond_it 1.173 r_mcbond_other 1.171 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.883 r_dihedral_angle_4_deg 17.414 r_dihedral_angle_3_deg 8.941 r_dihedral_angle_1_deg 6.87 r_angle_refined_deg 1.953 r_mcangle_it 1.665 r_angle_other_deg 1.62 r_mcbond_it 1.173 r_mcbond_other 1.171 r_chiral_restr 0.101 r_bond_refined_d 0.017 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 286 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing PHENIX refinement