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Nitrogenase MoFe protein from Azotobacter vinelandii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MIN PDB entry 3MIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 PEG 8000, sodium chloride, TRIS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.35 47.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.31 α = 90 b = 131.63 β = 108.37 c = 159.159 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 CCD ADSC QUANTUM 315 2002-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.992 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.16 100 95.6 0.09 0.078 10 2.5 1454519 1390520 1 1 12.34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.16 1.18 90 0.535 0.554 1.6 2.5 65290
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3MIN 1.16 50 1454519 1376724 13733 95.61 0.12349 0.12323 0.14924 RANDOM 15.839
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] 0.26 1.13 -0.43 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.902 r_sphericity_free 9.996 r_sphericity_bonded 6.275 r_dihedral_angle_1_deg 5.831 r_scangle_it 5.698 r_scbond_it 4.054 r_mcangle_it 2.894 r_rigid_bond_restr 2.613 r_mcbond_it 2.258 r_angle_refined_deg 2.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.902 r_sphericity_free 9.996 r_sphericity_bonded 6.275 r_dihedral_angle_1_deg 5.831 r_scangle_it 5.698 r_scbond_it 4.054 r_mcangle_it 2.894 r_rigid_bond_restr 2.613 r_mcbond_it 2.258 r_angle_refined_deg 2.251 r_nbtor_other 1.049 r_angle_other_deg 1.039 r_symmetry_hbond_refined 0.828 r_symmetry_vdw_refined 0.396 r_xyhbond_nbd_other 0.382 r_symmetry_vdw_other 0.373 r_nbd_refined 0.333 r_nbd_other 0.263 r_xyhbond_nbd_refined 0.225 r_chiral_restr 0.163 r_bond_refined_d 0.029 r_gen_planes_refined 0.013 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32171 Nucleic Acid Atoms Solvent Atoms 5021 Heterogen Atoms 192
Software Software Software Name Purpose MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling