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A. vinelandii nitrogenase MoFe protein Anc1b
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 293 0.1 M MES/imidazole at pH 6.5, 12.5% of (w/v) of polyethylene glycol 1000, 3350 and (v/v) 2-methyl-2,4-pentandiol each and 0.02 M of 1,6-hexanediol, 1-butanol, 1,4-butanediol, (RS)-1,2-propanediol, 2-propanol, and 1,3-propanediol, each
Crystal Properties Matthews coefficient Solvent content 2.26 45.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.083 α = 90 b = 128.984 β = 90 c = 209.445 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 EIGER2 X 9M 2023-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8856 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.824 109.828 94.4 0.068 0.997 7.5 13.1 91363
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 1.824 2.105 1.419 0.401 0.727
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 1.824 109.828 91363 4516 49.109 0.209 0.2063 0.2145 0.2686 0.2745 RANDOM 24.338
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] -1.3 -0.365 1.665
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.874 r_dihedral_angle_6_deg 14.799 r_dihedral_angle_1_deg 7.261 r_dihedral_angle_2_deg 6.919 r_lrange_it 3.97 r_lrange_other 3.917 r_scangle_it 2.291 r_scangle_other 2.291 r_angle_refined_deg 1.698 r_mcangle_it 1.598
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.874 r_dihedral_angle_6_deg 14.799 r_dihedral_angle_1_deg 7.261 r_dihedral_angle_2_deg 6.919 r_lrange_it 3.97 r_lrange_other 3.917 r_scangle_it 2.291 r_scangle_other 2.291 r_angle_refined_deg 1.698 r_mcangle_it 1.598 r_mcangle_other 1.598 r_scbond_it 1.354 r_scbond_other 1.354 r_mcbond_it 0.955 r_mcbond_other 0.955 r_angle_other_deg 0.583 r_nbd_other 0.25 r_nbd_refined 0.227 r_symmetry_nbd_refined 0.208 r_xyhbond_nbd_refined 0.207 r_symmetry_nbd_other 0.203 r_symmetry_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.183 r_chiral_restr 0.115 r_metal_ion_refined 0.108 r_symmetry_xyhbond_nbd_other 0.091 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.007 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 15974 Nucleic Acid Atoms Solvent Atoms 689 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing