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Structure of three-domain heme-Cu nitrite reductase from Ralstonia pickettii at 1.01 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z00 PDB ENTRY 2Z00
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 PEG, SODIUM CITRITE, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.48 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.177 α = 90 b = 128.177 β = 90 c = 86.314 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 2012-10-04 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 1.01 40 100 0.08 18 4.3 277728 6.4
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 1.01 1.05 99.9 0.62 2 3.4
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 2Z00 1.01 37.76 263699 14029 99.91 0.10962 0.10898 0.109 0.12182 0.1208 RANDOM 12.6
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] -0.01 -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.916 r_dihedral_angle_2_deg 39.116 r_dihedral_angle_4_deg 20.71 r_dihedral_angle_3_deg 12.101 r_sphericity_bonded 9.78 r_dihedral_angle_1_deg 6.782 r_rigid_bond_restr 4.678 r_angle_other_deg 2.207 r_angle_refined_deg 1.855 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.916 r_dihedral_angle_2_deg 39.116 r_dihedral_angle_4_deg 20.71 r_dihedral_angle_3_deg 12.101 r_sphericity_bonded 9.78 r_dihedral_angle_1_deg 6.782 r_rigid_bond_restr 4.678 r_angle_other_deg 2.207 r_angle_refined_deg 1.855 r_chiral_restr 0.117 r_gen_planes_other 0.018 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_bond_other_d 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3440 Nucleic Acid Atoms Solvent Atoms 794 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing