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Nitrogenase Cp1 at pH 6.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WES
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 PEG 3350, magnesium chloride, Tris/HCl, sodium dithionite
Crystal Properties Matthews coefficient Solvent content 2.66 53.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.477 α = 90 b = 147.963 β = 103.51 c = 116.694 γ = 90
Symmetry Space Group P 1 21 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 2015-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.72 113.46 98.5 0.105 13.5 6.8 238230
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.75 98.6 0.684 2.7 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 4WES 1.72 40 226300 11876 98.37 0.16058 0.15929 0.1686 0.18488 0.1923 RANDOM 29.257
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] -1.57 0.45 2.6 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.852 r_dihedral_angle_4_deg 21.554 r_dihedral_angle_3_deg 13.777 r_long_range_B_other 7.972 r_long_range_B_refined 7.941 r_scangle_other 6.976 r_dihedral_angle_1_deg 6.011 r_scbond_it 5.077 r_scbond_other 5.077 r_mcangle_it 4.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.852 r_dihedral_angle_4_deg 21.554 r_dihedral_angle_3_deg 13.777 r_long_range_B_other 7.972 r_long_range_B_refined 7.941 r_scangle_other 6.976 r_dihedral_angle_1_deg 6.011 r_scbond_it 5.077 r_scbond_other 5.077 r_mcangle_it 4.187 r_mcangle_other 4.187 r_mcbond_it 3.387 r_mcbond_other 3.387 r_angle_refined_deg 1.521 r_angle_other_deg 0.783 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 15106 Nucleic Acid Atoms Solvent Atoms 671 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement XDS data scaling Aimless data scaling PHASER phasing