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Crystal structure of nitric oxide bound D97N mutant 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 5OCF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 20% PEG3350, 0.2M SODIUM CITRATE, 20 mM BIS-TRIS-PROPANE-HCL PH7.5
Crystal Properties Matthews coefficient Solvent content 4.36 72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.46 α = 90 b = 180.46 β = 90 c = 180.46 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 2016-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
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 1.78 90.23 98.4 0.09 0.056 0.997 8 3.2 91145 19.3
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 1.78 1.88 99.4 0.657 0.424 0.504 1.7 3.2
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 5OCF 1.78 30.61 88375 2743 97.99 0.14416 0.14361 0.1543 0.1615 0.1702 RANDOM 25.629
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 35.444 r_dihedral_angle_4_deg 21.235 r_dihedral_angle_3_deg 12.807 r_long_range_B_refined 7.918 r_dihedral_angle_1_deg 6.599 r_long_range_B_other 6.221 r_scangle_other 3.153 r_mcangle_other 2.275 r_mcangle_it 2.273 r_scbond_it 2.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.444 r_dihedral_angle_4_deg 21.235 r_dihedral_angle_3_deg 12.807 r_long_range_B_refined 7.918 r_dihedral_angle_1_deg 6.599 r_long_range_B_other 6.221 r_scangle_other 3.153 r_mcangle_other 2.275 r_mcangle_it 2.273 r_scbond_it 2.064 r_scbond_other 2.064 r_angle_refined_deg 1.548 r_mcbond_it 1.518 r_mcbond_other 1.513 r_angle_other_deg 0.954 r_chiral_restr 0.104 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 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 670 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing