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Low-dose structure of Marinobacter nauticus nitrous oxide reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QNI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 303 15 % PEG 8000
0.6 M NaCl
0.1 M imidazole/malate
protein concentration: 14 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.61 52.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.26 α = 81.384 b = 69.375 β = 77.918 c = 153.188 γ = 88.608
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate Varimax HF 2020-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.498 23.501 91.4 0.026 0.026 1 12.1 2 381570 2 13.5
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 1.498 1.52 83.4 0.258 0.258 0.87 3 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.498 23.501 381568 19047 91.341 0.131 0.1298 0.13 0.1519 0.1522 16.34
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] -0.832 0.006 0.534 0.854 -0.079 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.107 r_dihedral_angle_3_deg 13.613 r_dihedral_angle_2_deg 8.049 r_dihedral_angle_1_deg 7.606 r_lrange_it 5.661 r_lrange_other 5.66 r_scangle_it 3.854 r_scangle_other 3.854 r_scbond_it 2.58 r_scbond_other 2.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.107 r_dihedral_angle_3_deg 13.613 r_dihedral_angle_2_deg 8.049 r_dihedral_angle_1_deg 7.606 r_lrange_it 5.661 r_lrange_other 5.66 r_scangle_it 3.854 r_scangle_other 3.854 r_scbond_it 2.58 r_scbond_other 2.58 r_angle_refined_deg 2.075 r_mcangle_other 1.742 r_mcangle_it 1.741 r_mcbond_it 1.233 r_mcbond_other 1.233 r_angle_other_deg 0.606 r_symmetry_xyhbond_nbd_refined 0.226 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.194 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.175 r_nbd_other 0.175 r_symmetry_nbd_refined 0.174 r_chiral_restr 0.112 r_metal_ion_refined 0.112 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_other 0.076 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18072 Nucleic Acid Atoms Solvent Atoms 3222 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement DENZO data reduction Aimless data scaling MOLREP phasing