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A. vinelandii nitrogenase MoFe protein Anc2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3U7Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 4.5% (w/v) of polyethylene glycol 2000, 3350, 4000 and polyethylene glycol mono methylether 5000, 0.1 M MES/NaOH at pH 6.5, 10% (v/v) of ethylene glycol and 0.15 M Mg acetate
Crystal Properties Matthews coefficient Solvent content 2.22 44.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.936 α = 90 b = 130.133 β = 90 c = 209.137 γ = 90
Symmetry Space Group P 21 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 EIGER X 16M 2022-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.816 110.49 95 0.2 0.998 10 13 121997
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.816 2.013 1.642 0.478 0.698
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.816 110.489 121997 6145 66.086 0.179 0.1762 0.1848 0.2254 0.2287 RANDOM 25.546
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] 0.191 0.073 -0.264
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.499 r_dihedral_angle_3_deg 13.474 r_dihedral_angle_other_3_deg 9.043 r_dihedral_angle_2_deg 7.342 r_dihedral_angle_1_deg 6.796 r_lrange_it 5.864 r_lrange_other 5.782 r_scangle_it 4.539 r_scangle_other 4.539 r_mcangle_it 3.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.499 r_dihedral_angle_3_deg 13.474 r_dihedral_angle_other_3_deg 9.043 r_dihedral_angle_2_deg 7.342 r_dihedral_angle_1_deg 6.796 r_lrange_it 5.864 r_lrange_other 5.782 r_scangle_it 4.539 r_scangle_other 4.539 r_mcangle_it 3.338 r_mcangle_other 3.338 r_scbond_it 2.905 r_scbond_other 2.905 r_mcbond_it 2.259 r_mcbond_other 2.259 r_angle_refined_deg 1.638 r_angle_other_deg 0.57 r_nbd_other 0.23 r_nbd_refined 0.222 r_symmetry_nbd_refined 0.195 r_symmetry_nbd_other 0.191 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.182 r_symmetry_xyhbond_nbd_refined 0.174 r_symmetry_xyhbond_nbd_other 0.129 r_metal_ion_refined 0.102 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_1 0.061 r_ncsr_local_group_2 0.049 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15926 Nucleic Acid Atoms Solvent Atoms 1298 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling PHASER phasing