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Crystal structure of core domain of four-domain heme-cupredoxin-Cu nitrite reductase from Bradyrhizobium sp. ORS 375
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, SITTING DROP 6.5 298 10% (w/v) PEG 8,000,
20% (v/v) 1,5-pentanediol,
0.1 M MOPSO/Bis-Tris pH6.5,
0.005 M Yttrium (III) chloride hexahydrate,
0.005 M Erbium (III) chloride hexahydrate,
0.005 M Terbium (III) chloride hexahydrate,
0.005 M Ytterbium (III) chloride hexahydrate
Crystal Properties Matthews coefficient Solvent content 2.39 48.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.141 α = 90 b = 125.141 β = 90 c = 125.141 γ = 90
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 PILATUS3 6M 2019-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 2.87 39.57 93.2 0.219 0.275 0.163 0.939 3.5 2.8 7073 29.2
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 2.87 3.03 88.8 0.481 0.607 0.362 0.738 1.7 2.6
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 2.87 39.57 6726 330 92.67 0.2257 0.2253 0.2251 0.2344 0.2344 RANDOM 23.882
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.341 r_dihedral_angle_3_deg 13.663 r_dihedral_angle_4_deg 10.431 r_dihedral_angle_1_deg 5.87 r_angle_refined_deg 0.653 r_chiral_restr 0.05 r_bond_refined_d 0.002 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2250 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 62
Software Software Software Name Purpose xia2 data scaling DIALS data scaling Aimless data scaling MOLREP phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction