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Crystal structure of as isolated three-domain copper-containing nitrite reductase from Hyphomicrobium denitrificans strain 1NES1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DV6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 20% (w/v) PEG 1,000,
0.1 M Sodium citrate tribasic dihydrate pH5.5,
0.1 M Lithium sulfate monohydrate
Crystal Properties Matthews coefficient Solvent content 2.2 44.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.072 α = 90 b = 77.072 β = 90 c = 754.548 γ = 120
Symmetry Space Group P 65 2 2
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 2019-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.05 66.75 98.7 0.121 0.084 0.995 3.5 4.3 85026 36.5
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 2.05 2.09 98.2 0.926 0.677 0.61 0.8 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 2DV6 2.05 66.58 80428 4195 98.29 0.2297 0.2271 0.2351 0.2789 0.2826 RANDOM 47.868
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] 2.1 1.05 2.1 -6.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.373 r_dihedral_angle_4_deg 23.051 r_dihedral_angle_3_deg 16.595 r_dihedral_angle_1_deg 8.63 r_angle_refined_deg 1.511 r_angle_other_deg 1.248 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.373 r_dihedral_angle_4_deg 23.051 r_dihedral_angle_3_deg 16.595 r_dihedral_angle_1_deg 8.63 r_angle_refined_deg 1.511 r_angle_other_deg 1.248 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9612 Nucleic Acid Atoms Solvent Atoms 528 Heterogen Atoms 9
Software Software Software Name Purpose DIALS data processing Aimless data scaling MOLREP phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction DIALS data scaling