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Structure of M92A variant of three-domain heme-Cu nitrite reductase from Ralstonia pickettii
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 20MM MES PH 6.5 20% PEG3350, 0.2 SODIUM CITRATE, 200 MM NACL, PROTEIN CONCENTRATION 7.5 MG/ML
Crystal Properties Matthews coefficient Solvent content 2.78 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.41 α = 90 b = 128.41 β = 90 c = 86.09 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 2012-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.87 32 98.9 0.12 7.1 5 43074 22.6
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 1.87 1.92 88.8 0.76 1.8 3
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 4AWW 1.87 40.14 40892 2170 99.98 0.14047 0.13898 0.1446 0.16822 0.1741 RANDOM 19.508
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] -0.52 -0.26 -0.52 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.018 r_dihedral_angle_4_deg 19.619 r_dihedral_angle_3_deg 13.237 r_dihedral_angle_1_deg 6.301 r_scangle_it 3.654 r_scbond_it 2.375 r_angle_refined_deg 1.522 r_mcangle_it 1.418 r_angle_other_deg 0.888 r_mcbond_it 0.801
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.018 r_dihedral_angle_4_deg 19.619 r_dihedral_angle_3_deg 13.237 r_dihedral_angle_1_deg 6.301 r_scangle_it 3.654 r_scbond_it 2.375 r_angle_refined_deg 1.522 r_mcangle_it 1.418 r_angle_other_deg 0.888 r_mcbond_it 0.801 r_mcbond_other 0.242 r_chiral_restr 0.092 r_bond_refined_d 0.016 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 3427 Nucleic Acid Atoms Solvent Atoms 457 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing