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Crystal structure of nitric oxide bound to three-domain heme-Cu nitrite reductase from Ralstonia pickettii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6F1Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 20% PEG3350, 0.2M SODIUM CITRATE, 20MM BIS-TRIS-PROPANE-HCL PH7.5
Crystal Properties Matthews coefficient Solvent content 4.6 72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.18 α = 90 b = 183.18 β = 90 c = 183.18 γ = 90
Symmetry Space Group I 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 2016-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.8 90 100 0.127 0.056 0.997 9.7 6.1 93990 32.09
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 99.8 1.056 0.512 0.362 1.4 5.2
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 FOURIER SYNTHESIS THROUGHOUT 6f1q 1.8 74.78 92042 1939 99.94 0.14957 0.14924 0.1606 0.16449 0.1767 RANDOM 27.118
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 35.03 r_dihedral_angle_4_deg 20.716 r_dihedral_angle_3_deg 12.693 r_long_range_B_refined 7.63 r_dihedral_angle_1_deg 6.547 r_long_range_B_other 6.05 r_scangle_other 2.836 r_mcangle_it 2.258 r_mcangle_other 2.258 r_scbond_it 1.851
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.03 r_dihedral_angle_4_deg 20.716 r_dihedral_angle_3_deg 12.693 r_long_range_B_refined 7.63 r_dihedral_angle_1_deg 6.547 r_long_range_B_other 6.05 r_scangle_other 2.836 r_mcangle_it 2.258 r_mcangle_other 2.258 r_scbond_it 1.851 r_scbond_other 1.85 r_mcbond_it 1.513 r_mcbond_other 1.511 r_angle_refined_deg 1.492 r_angle_other_deg 0.955 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3428 Nucleic Acid Atoms Solvent Atoms 665 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing