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Selenium incorporated nitrogenase MoFe-protein (Av1-Se2B) from A. vinelandii
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 291 PEG 8000, NaCl, Imidazole/Malate, Sodiumdithionite
Crystal Properties Matthews coefficient Solvent content 2.24 45.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.582 α = 90 b = 130.825 β = 108.85 c = 107.128 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 2015-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97918 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 1.6 38.76 97.8 0.151 9.5 7.1 256394
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 1.6 1.69 97.8 0.795 2.3 7.1
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 3U7Q 1.6 101.38 243657 12691 96.56 0.15292 0.15156 0.1637 0.17913 0.1893 RANDOM 13.776
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] 0.66 0.37 -0.53 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.584 r_sphericity_free 20.813 r_dihedral_angle_4_deg 19.58 r_dihedral_angle_3_deg 12.519 r_dihedral_angle_1_deg 5.969 r_sphericity_bonded 3.236 r_long_range_B_refined 1.781 r_long_range_B_other 1.781 r_angle_refined_deg 1.53 r_angle_other_deg 1.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.584 r_sphericity_free 20.813 r_dihedral_angle_4_deg 19.58 r_dihedral_angle_3_deg 12.519 r_dihedral_angle_1_deg 5.969 r_sphericity_bonded 3.236 r_long_range_B_refined 1.781 r_long_range_B_other 1.781 r_angle_refined_deg 1.53 r_angle_other_deg 1.484 r_scangle_other 0.82 r_rigid_bond_restr 0.711 r_mcangle_it 0.696 r_mcangle_other 0.696 r_scbond_it 0.665 r_scbond_other 0.665 r_mcbond_it 0.536 r_mcbond_other 0.536 r_chiral_restr 0.094 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15897 Nucleic Acid Atoms Solvent Atoms 1433 Heterogen Atoms 145
Software Software Software Name Purpose REFMAC refinement SCALA data scaling Coot model building XDS data scaling XDS data reduction MOLREP phasing