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Chlorite dismutase from Pseudomonas sp.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K90
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289 0.2M Ammonium citrate dibasic; 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.31 46.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.46 α = 90 b = 45.971 β = 129.3 c = 90.156 γ = 90
Symmetry Space Group C 1 2 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 2022-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.7749 PETRA III, EMBL c/o DESY P13 (MX1)
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 0.99 49.32 97.2 0.046 0.05 0.019 0.999 14.8 6.8 217930
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 0.99 1.02 92.6 2.346 2.532 0.944 0.364 7
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 MOLECULAR REPLACEMENT THROUGHOUT 0.99 49.32 215927 2000 97.2 0.14365 0.1435 0.1416 0.16067 0.1584 RANDOM 18.259
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] 0.05 -0.03 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.727 r_dihedral_angle_2_deg 8.898 r_rigid_bond_restr 8.424 r_dihedral_angle_1_deg 6.308 r_long_range_B_refined 3.983 r_mcangle_other 2.925 r_mcangle_it 2.923 r_long_range_B_other 2.827 r_mcbond_other 2.773 r_mcbond_it 2.772
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.727 r_dihedral_angle_2_deg 8.898 r_rigid_bond_restr 8.424 r_dihedral_angle_1_deg 6.308 r_long_range_B_refined 3.983 r_mcangle_other 2.925 r_mcangle_it 2.923 r_long_range_B_other 2.827 r_mcbond_other 2.773 r_mcbond_it 2.772 r_scangle_other 2.063 r_angle_refined_deg 1.727 r_scbond_it 1.512 r_scbond_other 1.512 r_angle_other_deg 0.636 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_gen_planes_other 0.008 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2978 Nucleic Acid Atoms Solvent Atoms 741 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing