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MgADP-bound Fe protein of the iron-only nitrogenase from Azotobacter vinelandii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Q93
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.05 M magnesium chloride, 0.1 M HEPES/NaOH pH7.0, PEG 550
Crystal Properties Matthews coefficient Solvent content 2.32 47.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.677 α = 68.57 b = 80.366 β = 75.85 c = 80.024 γ = 76.03
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 2018-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 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 1.79 73.48 90.5 0.997 6.9 3.5 67524
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 1.8 1.99 0.71
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 6Q93 1.79 73.48 64307 3226 66.39 0.1995 0.197 0.2021 0.2486 0.2504 RANDOM 31.013
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] -0.12 -0.08 -0.01 0.11 0.11 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.218 r_dihedral_angle_4_deg 17.443 r_dihedral_angle_3_deg 16.196 r_dihedral_angle_1_deg 7.007 r_angle_refined_deg 1.501 r_angle_other_deg 1.285 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.218 r_dihedral_angle_4_deg 17.443 r_dihedral_angle_3_deg 16.196 r_dihedral_angle_1_deg 7.007 r_angle_refined_deg 1.501 r_angle_other_deg 1.285 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8322 Nucleic Acid Atoms Solvent Atoms 762 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction autoPROC data scaling MOLREP phasing