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PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of HAO1 in complex with Z2856434894
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 2.35 47.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.677 α = 90 b = 97.677 β = 90 c = 80.414 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 2018-01-28 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 1.34 26.2 94.8 0.05 0.055 0.022 0.999 19.4 5.4 80351
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 1.34 1.37 61.8 0.638 0.791 0.455 0.802 2.7 3842
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 1.34 69.07 76297 4052 94.75 0.1663 0.1648 0.168 0.1927 0.1947 RANDOM 17.532
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] -0.72 -0.72 1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.105 r_dihedral_angle_4_deg 14.223 r_sphericity_free 12.285 r_dihedral_angle_3_deg 12.163 r_dihedral_angle_1_deg 6.308 r_sphericity_bonded 5.961 r_rigid_bond_restr 3.201 r_mcangle_it 2.073 r_angle_refined_deg 1.875 r_mcbond_other 1.725
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.105 r_dihedral_angle_4_deg 14.223 r_sphericity_free 12.285 r_dihedral_angle_3_deg 12.163 r_dihedral_angle_1_deg 6.308 r_sphericity_bonded 5.961 r_rigid_bond_restr 3.201 r_mcangle_it 2.073 r_angle_refined_deg 1.875 r_mcbond_other 1.725 r_mcbond_it 1.724 r_angle_other_deg 1.081 r_chiral_restr 0.125 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2669 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing