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IDS-oxidized 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 IDS
Crystal Properties Matthews coefficient Solvent content 2.08 40.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.806 α = 90 b = 74.579 β = 90 c = 75.02 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 1.0332 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 1.58 52.891 98.7 0.057 0.059 0.016 31.2 13.2 35382
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 1.58 1.67 97.5 0.879 0.879 0.915 0.25 0.9 12.9
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 1.58 37.54 33581 1740 98.35 0.1651 0.1638 0.1761 0.1877 0.2009 RANDOM 22.987
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] 0.02 0.16 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.558 r_dihedral_angle_4_deg 14.633 r_sphericity_free 12.585 r_dihedral_angle_3_deg 11.464 r_sphericity_bonded 9.148 r_dihedral_angle_1_deg 6.376 r_angle_refined_deg 1.544 r_angle_other_deg 1.411 r_rigid_bond_restr 1.384 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.558 r_dihedral_angle_4_deg 14.633 r_sphericity_free 12.585 r_dihedral_angle_3_deg 11.464 r_sphericity_bonded 9.148 r_dihedral_angle_1_deg 6.376 r_angle_refined_deg 1.544 r_angle_other_deg 1.411 r_rigid_bond_restr 1.384 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2140 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing PDB_EXTRACT data extraction