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Dithionite-reduced ADP-bound 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 7.5 298 40% PEG 400, 0.17 mM Cymal 7, 0.1 M HEPES pH 7.5, 5 mM dithionite
Crystal Properties Matthews coefficient Solvent content 2.08 41.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.587 α = 90 b = 74.63 β = 90 c = 75.398 γ = 90
Symmetry Space Group P 2 21 21
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 2014-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.8856 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 1.13 53.041 100 0.068 0.071 0.02 17.6 12.9 96897
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 1.13 1.19 99.9 0.799 0.799 0.835 0.239 1 11.9
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 1.13 39.04 92016 4770 99.93 0.1464 0.1459 0.1461 0.157 0.1474 RANDOM 16.113
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] -0.24 0.26 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.199 r_dihedral_angle_4_deg 16.939 r_sphericity_free 14.403 r_dihedral_angle_3_deg 12.483 r_sphericity_bonded 6.865 r_dihedral_angle_1_deg 6.318 r_angle_refined_deg 1.466 r_angle_other_deg 1.389 r_rigid_bond_restr 0.822 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.199 r_dihedral_angle_4_deg 16.939 r_sphericity_free 14.403 r_dihedral_angle_3_deg 12.483 r_sphericity_bonded 6.865 r_dihedral_angle_1_deg 6.318 r_angle_refined_deg 1.466 r_angle_other_deg 1.389 r_rigid_bond_restr 0.822 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2140 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing