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PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of HAO1 in complex with Z31792168
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NZL 2NZL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.75 293 0.1M MIB pH 5.75 - 7.0, 27.5-35% PEG1000
Crystal Properties Matthews coefficient Solvent content 2.38 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.78 α = 90 b = 97.78 β = 90 c = 81.268 γ = 90
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 PILATUS 6M 2018-01-27 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.2 26.33 82.2 0.035 0.039 0.015 0.999 25 4.7 97888
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.23 15.7 0.357 0.505 0.357 0.787 1.1 1369
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2NZL 1.2 69.14 92992 4888 82.2 0.1641 0.163 0.1635 0.1829 0.1827 RANDOM 14.218
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] -0.4 -0.4 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.111 r_dihedral_angle_4_deg 14.641 r_dihedral_angle_3_deg 11.798 r_sphericity_free 10.509 r_dihedral_angle_1_deg 6.181 r_sphericity_bonded 3.987 r_rigid_bond_restr 2.078 r_angle_refined_deg 1.639 r_mcangle_it 1.314 r_mcbond_it 1.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.111 r_dihedral_angle_4_deg 14.641 r_dihedral_angle_3_deg 11.798 r_sphericity_free 10.509 r_dihedral_angle_1_deg 6.181 r_sphericity_bonded 3.987 r_rigid_bond_restr 2.078 r_angle_refined_deg 1.639 r_mcangle_it 1.314 r_mcbond_it 1.086 r_mcbond_other 1.082 r_angle_other_deg 1.033 r_chiral_restr 0.103 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2723 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing