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Structure of the F306C mutant of nitrite reductase from Achromobacter xylosoxidans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OE1 PDB ENTRY 1OE1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.1 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.99 α = 90 b = 89.99 β = 90 c = 289.45 γ = 120
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 PILATUS 6M MIRRORS 2011-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.69 46.47 99.9 0.06 11.6 5 97508 18.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.79 99 0.58 2 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 1OE1 1.7 46.47 90508 4764 99.16 0.18279 0.18112 0.1886 0.21482 0.2189 RANDOM 25.455
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] 0.29 0.14 0.29 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.669 r_dihedral_angle_4_deg 17.274 r_dihedral_angle_3_deg 13.572 r_dihedral_angle_1_deg 7.173 r_mcangle_it 2.466 r_scbond_it 2.117 r_mcbond_it 1.759 r_mcbond_other 1.759 r_angle_refined_deg 1.672 r_angle_other_deg 0.836
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.669 r_dihedral_angle_4_deg 17.274 r_dihedral_angle_3_deg 13.572 r_dihedral_angle_1_deg 7.173 r_mcangle_it 2.466 r_scbond_it 2.117 r_mcbond_it 1.759 r_mcbond_other 1.759 r_angle_refined_deg 1.672 r_angle_other_deg 0.836 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5124 Nucleic Acid Atoms Solvent Atoms 602 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing