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Structure of chlorite dismutase from Candidatus Nitrospira defluvii R173K mutant
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 4 295 0.4-0.6M ammonium sulphate, 0.1M citric acid, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.02 59.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.41 α = 90 b = 113.88 β = 118.02 c = 119.87 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 CCD ADSC QUANTUM 210 2009-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.933 ESRF ID14-1
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 2.7 106 91.5 44825
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.7 2.77 80.9
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 2.7 43.72 42510 42510 2256 99.84 0.21831 0.21831 0.21609 0.2212 0.25798 0.2675 RANDOM 77.041
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] -0.3 -8.42 -2.13 -5.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.342 r_dihedral_angle_4_deg 19.801 r_dihedral_angle_3_deg 18.062 r_dihedral_angle_1_deg 5.568 r_scangle_it 1.694 r_angle_refined_deg 1.325 r_scbond_it 1.162 r_angle_other_deg 0.909 r_mcangle_it 0.574 r_mcbond_it 0.457
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.342 r_dihedral_angle_4_deg 19.801 r_dihedral_angle_3_deg 18.062 r_dihedral_angle_1_deg 5.568 r_scangle_it 1.694 r_angle_refined_deg 1.325 r_scbond_it 1.162 r_angle_other_deg 0.909 r_mcangle_it 0.574 r_mcbond_it 0.457 r_symmetry_hbond_refined 0.4 r_symmetry_vdw_refined 0.254 r_symmetry_vdw_other 0.253 r_nbd_refined 0.211 r_mcbond_other 0.21 r_nbd_other 0.191 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.175 r_xyhbond_nbd_other 0.144 r_nbtor_other 0.086 r_chiral_restr 0.071 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_metal_ion_refined r_metal_ion_other 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 9585 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 320
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling