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Dithionite-reduced nucleotide-free form of the nitrogenase Fe-protein from A. vinelandii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G5P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 of 40% PEG 1000, 0.2 M NaCl, 0.1 M MES/OH pH 6.5, 10% 2,2,2-trifluoroethanol, 5 mM dithionite
Crystal Properties Matthews coefficient Solvent content 2.14 42.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.62 α = 90 b = 45.199 β = 96.58 c = 108.772 γ = 90
Symmetry Space Group C 1 2 1
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 6M 2017-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.0 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.756 108.055 96.5 0.045 0.049 0.019 22 6.7 48484
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.756 1.85 81.8 0.208 0.208 0.228 0.092 3.6 5.7
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 1G5P 1.756 39.29 46085 2369 96.18 0.1729 0.1708 0.1813 0.213 0.2215 RANDOM 31.362
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] 0.13 -0.84 0.67 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.72 r_sphericity_free 21.645 r_dihedral_angle_4_deg 16.111 r_dihedral_angle_3_deg 14.427 r_sphericity_bonded 12.071 r_dihedral_angle_1_deg 6.442 r_angle_refined_deg 1.703 r_angle_other_deg 1.597 r_rigid_bond_restr 1.283 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.72 r_sphericity_free 21.645 r_dihedral_angle_4_deg 16.111 r_dihedral_angle_3_deg 14.427 r_sphericity_bonded 12.071 r_dihedral_angle_1_deg 6.442 r_angle_refined_deg 1.703 r_angle_other_deg 1.597 r_rigid_bond_restr 1.283 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4093 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing PDB_EXTRACT data extraction