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CRYSTAL STRUCTURE OF AS-ISOLATED M148L 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 277 0.1 M Bis-tris propane pH 6.3, 0.1 M sodium citrate, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.73 54.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.952 α = 90 b = 127.952 β = 90 c = 86.249 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 2020-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978565 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 1.32 46.66 99.4 0.137 0.152 0.067 0.995 6.4 5.1 124091
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 1.32 1.34 87.9 1.888 2.124 0.961 0.265 0.7 4.5
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 (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 1.32 46.66 118239 5839 99.38 0.1353 0.13401 0.1318 0.16176 0.1613 RANDOM 17.23
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] 0.99 0.5 0.99 -3.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.941 r_dihedral_angle_4_deg 19.342 r_dihedral_angle_3_deg 11.644 r_dihedral_angle_1_deg 7.054 r_long_range_B_refined 3.272 r_rigid_bond_restr 3.245 r_long_range_B_other 2.494 r_scangle_other 1.738 r_angle_refined_deg 1.683 r_scbond_other 1.592
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.941 r_dihedral_angle_4_deg 19.342 r_dihedral_angle_3_deg 11.644 r_dihedral_angle_1_deg 7.054 r_long_range_B_refined 3.272 r_rigid_bond_restr 3.245 r_long_range_B_other 2.494 r_scangle_other 1.738 r_angle_refined_deg 1.683 r_scbond_other 1.592 r_scbond_it 1.591 r_angle_other_deg 1.43 r_mcangle_it 1.41 r_mcangle_other 1.41 r_mcbond_it 1.126 r_mcbond_other 1.104 r_chiral_restr 0.103 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.008 r_gen_planes_other 0.008 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3423 Nucleic Acid Atoms Solvent Atoms 736 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction Coot model building