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Structure of three-domain heme-Cu nitrite reductase from Ralstonia pickettii at 1.6 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AWW PDB ENTRY 4AWW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 PEG, SODIUM CITRITE, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.4 49.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.812 α = 90 b = 185.812 β = 90 c = 185.812 γ = 90
Symmetry Space Group P 21 3
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 2012-03-31 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 1.6 25 99.9 0.07 25 8 278689 20.7
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 1.6 1.66 100 0.8 2 6.2
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 4AWW 1.6 25 264055 14041 99.82 0.16453 0.16296 0.1681 0.19411 0.1973 RANDOM 17.703
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.195 r_dihedral_angle_4_deg 18.529 r_dihedral_angle_3_deg 12.653 r_dihedral_angle_1_deg 6.541 r_scangle_it 3.358 r_scbond_it 2.16 r_angle_refined_deg 1.532 r_mcangle_it 1.356 r_angle_other_deg 0.92 r_mcbond_it 0.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.195 r_dihedral_angle_4_deg 18.529 r_dihedral_angle_3_deg 12.653 r_dihedral_angle_1_deg 6.541 r_scangle_it 3.358 r_scbond_it 2.16 r_angle_refined_deg 1.532 r_mcangle_it 1.356 r_angle_other_deg 0.92 r_mcbond_it 0.799 r_mcbond_other 0.243 r_chiral_restr 0.093 r_bond_refined_d 0.015 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_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 13728 Nucleic Acid Atoms Solvent Atoms 2470 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing