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PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of HAO1 in complex with Z1407672867
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 47.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.54 α = 90 b = 97.54 β = 90 c = 80.646 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 2018-01-29 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 1.42 26.21 99.8 0.045 0.049 0.019 0.999 19.1 5.7 71180
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 1.42 1.46 98.5 0.551 0.65 0.34 0.754 3.5 5192
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 1.42 68.97 67577 3597 99.84 0.157 0.1554 0.1566 0.1868 0.188 RANDOM 19.117
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] -0.66 -0.66 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.259 r_dihedral_angle_4_deg 13.928 r_sphericity_free 13.621 r_dihedral_angle_3_deg 12.377 r_sphericity_bonded 7.5 r_dihedral_angle_1_deg 6.163 r_mcangle_it 2.512 r_rigid_bond_restr 2.286 r_mcbond_it 2.014 r_mcbond_other 1.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.259 r_dihedral_angle_4_deg 13.928 r_sphericity_free 13.621 r_dihedral_angle_3_deg 12.377 r_sphericity_bonded 7.5 r_dihedral_angle_1_deg 6.163 r_mcangle_it 2.512 r_rigid_bond_restr 2.286 r_mcbond_it 2.014 r_mcbond_other 1.997 r_angle_refined_deg 1.65 r_angle_other_deg 1.042 r_chiral_restr 0.11 r_bond_refined_d 0.014 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 2715 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing