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Structure of chlorite dismutase from Candidatus Nitrospira defluvii in complex with cyanide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other IN-HOUSE MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 1.4M sodium/potassium phosphate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.02 59.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.49 α = 90 b = 145.49 β = 90 c = 136.011 γ = 120
Symmetry Space Group P 32 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 CCD ADSC QUANTUM 4 2008-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.94 125 99.2 122022 121046
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.94 1.99 99.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 IN-HOUSE MODEL 1.94 32.836 114958 114958 6084 98.92 0.17866 0.17866 0.1769 0.1974 0.21152 0.2271 RANDOM 38.845
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] -0.78 -0.39 -0.78 1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.165 r_dihedral_angle_4_deg 17.728 r_dihedral_angle_3_deg 14.69 r_dihedral_angle_1_deg 6.105 r_scangle_it 2.856 r_scbond_it 1.79 r_angle_refined_deg 1.322 r_mcangle_it 1.19 r_angle_other_deg 0.844 r_mcbond_it 0.647
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.165 r_dihedral_angle_4_deg 17.728 r_dihedral_angle_3_deg 14.69 r_dihedral_angle_1_deg 6.105 r_scangle_it 2.856 r_scbond_it 1.79 r_angle_refined_deg 1.322 r_mcangle_it 1.19 r_angle_other_deg 0.844 r_mcbond_it 0.647 r_mcbond_other 0.174 r_chiral_restr 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9620 Nucleic Acid Atoms Solvent Atoms 931 Heterogen Atoms 393
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling