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Structure of chlorite dismutase from Candidatus Nitrospira defluvii R173A 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 4.6 295 1.4M ammonium phosphate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.06 59.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.74 α = 90 b = 113.62 β = 118.94 c = 120.52 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 4 2009-02-26 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 2.6 105.4 92.1 50785
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.6 2.67 79.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT IN-HOUSE MODEL 2.6 44.39 48167 48167 2577 99.9 0.2142 0.2142 0.212 0.25434 0.2826 RANDOM 73.031
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] 0.34 -4.3 -1.83 -2.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.763 r_dihedral_angle_4_deg 18.566 r_dihedral_angle_3_deg 16.864 r_dihedral_angle_1_deg 5.612 r_scangle_it 1.769 r_angle_refined_deg 1.243 r_scbond_it 1.221 r_angle_other_deg 0.881 r_mcangle_it 0.721 r_mcbond_it 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.763 r_dihedral_angle_4_deg 18.566 r_dihedral_angle_3_deg 16.864 r_dihedral_angle_1_deg 5.612 r_scangle_it 1.769 r_angle_refined_deg 1.243 r_scbond_it 1.221 r_angle_other_deg 0.881 r_mcangle_it 0.721 r_mcbond_it 0.61 r_symmetry_hbond_refined 0.232 r_nbd_refined 0.209 r_nbd_other 0.187 r_symmetry_vdw_refined 0.186 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.178 r_symmetry_vdw_other 0.17 r_mcbond_other 0.151 r_nbtor_other 0.086 r_chiral_restr 0.067 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other 0.001 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 9565 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 315
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling