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CRYSTAL STRUCTURE OF REDUCED F295L 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 3.22 61.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.961 α = 90 b = 127.961 β = 90 c = 86.602 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 2020-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.80001 Diamond I04
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 1.33 37.74 96.1 0.085 0.096 0.045 0.998 8 4.3 116526
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 1.33 1.35 71.8 1.072 1.319 0.754 0.363 0.8 2.5
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 1.331 37.735 116451 5922 96.07 0.113 0.1118 0.1118 0.1405 0.1404 RANDOM 17.87
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] 0.182 0.091 0.182 -0.59
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.033 r_dihedral_angle_6_deg 15.577 r_lrange_other 13.792 r_dihedral_angle_3_deg 11.947 r_dihedral_angle_2_deg 9.977 r_scangle_it 8.399 r_scangle_other 8.399 r_dihedral_angle_1_deg 7.126 r_mcangle_other 6.31 r_mcangle_it 6.243
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.033 r_dihedral_angle_6_deg 15.577 r_lrange_other 13.792 r_dihedral_angle_3_deg 11.947 r_dihedral_angle_2_deg 9.977 r_scangle_it 8.399 r_scangle_other 8.399 r_dihedral_angle_1_deg 7.126 r_mcangle_other 6.31 r_mcangle_it 6.243 r_scbond_other 5.914 r_scbond_it 5.913 r_mcbond_it 4.636 r_mcbond_other 4.415 r_rigid_bond_restr 4.007 r_angle_refined_deg 1.859 r_angle_other_deg 0.657 r_nbd_refined 0.261 r_symmetry_xyhbond_nbd_refined 0.24 r_xyhbond_nbd_refined 0.224 r_nbd_other 0.203 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.174 r_symmetry_nbd_refined 0.158 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_other 0.026 r_symmetry_metal_ion_refined 0.018 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3425 Nucleic Acid Atoms Solvent Atoms 691 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction Coot model building REFMAC phasing