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CRYSTAL STRUCTURE OF REDUCED WILD TYPE 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 2.68 54.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.842 α = 90 b = 127.842 β = 90 c = 86.337 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 2021-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.87000 SOLEIL PROXIMA 1
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 1.17 37.685 100 0.089 0.099 0.044 0.998 7.9 4.9 177553 9.6
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 1.17 1.19 100 1.642 1.846 0.836 0.354 0.9 4.8
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 1.17 37.685 177460 8797 99.944 0.123 0.1217 0.1217 0.1461 0.1462 RANDOM 16.971
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] 0.118 0.059 0.118 -0.384
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.016 r_dihedral_angle_6_deg 16.202 r_lrange_other 15.712 r_dihedral_angle_3_deg 11.725 r_scangle_it 8.583 r_scangle_other 8.577 r_dihedral_angle_2_deg 8.068 r_dihedral_angle_1_deg 7.016 r_scbond_it 6.157 r_scbond_other 6.148
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.016 r_dihedral_angle_6_deg 16.202 r_lrange_other 15.712 r_dihedral_angle_3_deg 11.725 r_scangle_it 8.583 r_scangle_other 8.577 r_dihedral_angle_2_deg 8.068 r_dihedral_angle_1_deg 7.016 r_scbond_it 6.157 r_scbond_other 6.148 r_mcangle_other 5.216 r_mcangle_it 5.209 r_rigid_bond_restr 3.963 r_mcbond_it 3.838 r_mcbond_other 3.816 r_angle_refined_deg 1.883 r_angle_other_deg 0.69 r_symmetry_nbd_refined 0.263 r_xyhbond_nbd_refined 0.245 r_nbd_refined 0.24 r_symmetry_xyhbond_nbd_refined 0.219 r_symmetry_xyhbond_nbd_other 0.212 r_nbd_other 0.206 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.18 r_chiral_restr 0.118 r_symmetry_nbtor_other 0.087 r_symmetry_metal_ion_refined 0.038 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_xyhbond_nbd_other 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3423 Nucleic Acid Atoms Solvent Atoms 711 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction Coot model building REFMAC phasing