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CRYSTAL STRUCTURE OF NITRIC OXIDE-TREATED Q262N 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 3ZIY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.7 277 100 mM bis-tris propane pH 7.7, 200 mM sodium citrate, and 22% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.8 56.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.069 α = 90 b = 128.069 β = 90 c = 86.352 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 EIGER X 16M 2019-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.09 37.74 87.2 0.046 0.055 0.03 0.999 9.2 2.5 216270
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.14 1.16 82.9 0.907 1.143 0.684 0.374 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.09 37.74 216270 10975 98.146 0.107 0.1066 0.1066 0.1223 0.1222 RANDOM 15.283
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] -0.127 -0.063 -0.127 0.412
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.705 r_dihedral_angle_6_deg 15.835 r_lrange_other 12.457 r_dihedral_angle_3_deg 11.149 r_dihedral_angle_2_deg 8.715 r_dihedral_angle_1_deg 7.063 r_scangle_it 6.345 r_scangle_other 6.345 r_mcangle_other 4.54 r_mcangle_it 4.531
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.705 r_dihedral_angle_6_deg 15.835 r_lrange_other 12.457 r_dihedral_angle_3_deg 11.149 r_dihedral_angle_2_deg 8.715 r_dihedral_angle_1_deg 7.063 r_scangle_it 6.345 r_scangle_other 6.345 r_mcangle_other 4.54 r_mcangle_it 4.531 r_scbond_other 4.349 r_scbond_it 4.348 r_mcbond_it 3.095 r_mcbond_other 3.069 r_rigid_bond_restr 2.967 r_angle_refined_deg 1.775 r_angle_other_deg 0.632 r_symmetry_xyhbond_nbd_refined 0.251 r_symmetry_nbd_refined 0.248 r_nbd_other 0.233 r_nbd_refined 0.225 r_xyhbond_nbd_refined 0.221 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.176 r_metal_ion_refined 0.133 r_chiral_restr 0.098 r_symmetry_xyhbond_nbd_other 0.087 r_symmetry_nbtor_other 0.086 r_symmetry_metal_ion_refined 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3428 Nucleic Acid Atoms Solvent Atoms 821 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling Coot model building REFMAC phasing