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Nitrogenase MoFeP from Gluconacetobacter diazotrophicus in dithionite reduced state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M1N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 45% 2-methyl-2,4-pentadiol (MPD) , 300 mM NaCl, 100 mM Na Cacodylate, pH 6.5, 1 mM Spermine, 0.1% Zwittergent, and 5 mM Na2S2O4
Crystal Properties Matthews coefficient Solvent content 3 59.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 202.598 α = 90 b = 202.598 β = 90 c = 132.567 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 PIXEL DECTRIS PILATUS 6M 2016-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.98 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 1.83 143.26 100 0.4208 0.4288 0.976 12.85 27.2 240200 14.27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.895 100 1.434 0.815 1.46 27.8
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 1M1N 1.83 143.26 228228 11943 99.97 0.12972 0.12864 0.1421 0.15039 0.1625 RANDOM 17.981
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] -0.37 -0.37 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.23 r_dihedral_angle_4_deg 18.405 r_dihedral_angle_3_deg 13.226 r_long_range_B_refined 6.714 r_long_range_B_other 6.235 r_dihedral_angle_1_deg 6.132 r_scangle_other 4.705 r_scbond_it 3.091 r_scbond_other 3.091 r_angle_refined_deg 2.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.23 r_dihedral_angle_4_deg 18.405 r_dihedral_angle_3_deg 13.226 r_long_range_B_refined 6.714 r_long_range_B_other 6.235 r_dihedral_angle_1_deg 6.132 r_scangle_other 4.705 r_scbond_it 3.091 r_scbond_other 3.091 r_angle_refined_deg 2.015 r_mcangle_it 2.014 r_mcangle_other 2.014 r_angle_other_deg 1.79 r_mcbond_it 1.455 r_mcbond_other 1.455 r_chiral_restr 0.148 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.007 r_gen_planes_other 0.005 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15640 Nucleic Acid Atoms Solvent Atoms 1979 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data scaling Aimless data scaling PHASER phasing