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Structure of chlorite dismutase from Candidatus Nitrospira defluvii in complex with imidazole
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 3.04 59.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.67 α = 90 b = 145.67 β = 90 c = 136.44 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 2008-11-16 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 1.85 126 97 276446 268021
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.85 1.9 90.7
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 1.85 47.68 134596 134596 7117 99.7 0.18148 0.18148 0.17998 0.1846 0.20988 0.2125 RANDOM 32.5
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] -0.39 -0.19 -0.39 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.047 r_dihedral_angle_4_deg 19.327 r_dihedral_angle_3_deg 14.412 r_dihedral_angle_1_deg 5.89 r_scangle_it 3.023 r_angle_other_deg 2.187 r_scbond_it 1.986 r_angle_refined_deg 1.399 r_mcangle_it 1.255 r_mcbond_it 0.721
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.047 r_dihedral_angle_4_deg 19.327 r_dihedral_angle_3_deg 14.412 r_dihedral_angle_1_deg 5.89 r_scangle_it 3.023 r_angle_other_deg 2.187 r_scbond_it 1.986 r_angle_refined_deg 1.399 r_mcangle_it 1.255 r_mcbond_it 0.721 r_mcbond_other 0.118 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9595 Nucleic Acid Atoms Solvent Atoms 913 Heterogen Atoms 351
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling