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Insights into substrate binding at FeMo-cofactor in nitrogenase from the structure of an alpha-70Ile MoFe protein variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2MIN PDB entry 2MIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 8 298 30% PEG 4000, 100mM Tris-HCl pH 8.0, 170-190mM Sodium molybdate and 1mM Dithionite, LIQUID DIFFUSION, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.2 44.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.019 α = 90 b = 129.458 β = 109.01 c = 107.088 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 MARMOSAIC 325 mm CCD mirrors 2008-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.8900 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.23 50 99.9 0.115 11.8 3.8 187881 2.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.23 2.33 0.233 3.5 18797
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 PDB entry 2MIN 2.23 50 90665 4778 98.46 0.207 0.20449 0.2092 0.25433 0.2602 RANDOM 31.399
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] 1.66 0.38 0.23 -1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.469 r_dihedral_angle_4_deg 24.593 r_dihedral_angle_3_deg 15.597 r_scangle_it 7.743 r_dihedral_angle_1_deg 5.811 r_scbond_it 5.386 r_angle_refined_deg 3.226 r_mcbond_it 2.29 r_mcangle_it 2.138 r_angle_other_deg 1.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.469 r_dihedral_angle_4_deg 24.593 r_dihedral_angle_3_deg 15.597 r_scangle_it 7.743 r_dihedral_angle_1_deg 5.811 r_scbond_it 5.386 r_angle_refined_deg 3.226 r_mcbond_it 2.29 r_mcangle_it 2.138 r_angle_other_deg 1.279 r_mcbond_other 0.372 r_xyhbond_nbd_other 0.237 r_symmetry_vdw_other 0.231 r_symmetry_vdw_refined 0.213 r_symmetry_hbond_refined 0.194 r_nbd_other 0.191 r_nbd_refined 0.19 r_nbtor_refined 0.173 r_metal_ion_refined 0.167 r_xyhbond_nbd_refined 0.142 r_nbtor_other 0.082 r_chiral_restr 0.06 r_bond_refined_d 0.011 r_bond_other_d 0.007 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15778 Nucleic Acid Atoms Solvent Atoms 830 Heterogen Atoms 96
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling