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IPNS H270D variant in complex with Fe and ACV under anaerobic conditions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other PDB 6ZAE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 8.3 298 1.7 M Li2SO4, 0.1 M Tris pH 8.3
Crystal Properties Matthews coefficient Solvent content 2.02 39.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.589 α = 90 b = 74.193 β = 90 c = 100.833 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 XE 16M 2022-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9227 Diamond I04
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 1.53 37.65 100 0.222 0.23 0.062 0.998 7 13.5 46843 18.28
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 1.53 1.56 99.5 3.234 3.36 0.903 0.494 0.4 13.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6ZAE 1.53 37.65 1.33 46691 2251 99.73 0.2154 0.2134 0.2133 0.2548 0.2538 23.75
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.7839 f_angle_d 0.824 f_chiral_restr 0.0562 f_plane_restr 0.007 f_bond_d 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2601 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 50
Software Software Software Name Purpose PHENIX refinement xia2 data reduction DIALS data scaling PHASER phasing