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Vanadium nitrogenase VFe protein, high CO state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ADR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Tris/HCl pH 7.5, magnesium chloride, ethylene glycol, PEG 8000, sodium dithionite
Crystal Properties Matthews coefficient Solvent content 2.48 50.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.521 α = 84 b = 80.041 β = 72.48 c = 107.21 γ = 75.03
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 PILATUS 2M-F 2018-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.977944 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.05 48.39 93.3 0.999 9.7 7 1006898
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.05 1.07 0.444
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 7ADR 1.05 48.39 956836 49972 93.25 0.1255 0.1244 0.1243 0.1459 0.1457 RANDOM 14.508
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] 0.05 -0.05 -0.17 -0.12 0.13 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.356 r_dihedral_angle_4_deg 18.869 r_dihedral_angle_3_deg 12.269 r_dihedral_angle_1_deg 6.501 r_rigid_bond_restr 5.984 r_angle_refined_deg 3.08 r_angle_other_deg 1.857 r_chiral_restr 0.49 r_bond_refined_d 0.023 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.356 r_dihedral_angle_4_deg 18.869 r_dihedral_angle_3_deg 12.269 r_dihedral_angle_1_deg 6.501 r_rigid_bond_restr 5.984 r_angle_refined_deg 3.08 r_angle_other_deg 1.857 r_chiral_restr 0.49 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16687 Nucleic Acid Atoms Solvent Atoms 2602 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling REFMAC phasing