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High-resolution structure of the D. fructosovorans NiFe-hydrogenase L122A mutant after exposure to air
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.1 298 VAPOR DIFFUSION, ANAEROBIC GROWTH, 298 K, PEG 6000, MES, HEPES, CRYSTAL EXPOSED 3 DAYS TO AIR, PH 6.1
Crystal Properties Matthews coefficient Solvent content 2.03 39.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.7 α = 90 b = 100.9 β = 105.9 c = 116.7 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 315r 2009-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.42 44.1 97.5 0.052 11.48 3.59 264128 -3 16.7
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 1.42 1.5 86.4 0.337 2.4 2.83
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 (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 1.42 30 250702 13409 97.51 0.12168 0.11983 0.1205 0.15633 0.157 RANDOM 13.199
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] 0.32 0.17 -0.22 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.49 r_sphericity_free 25.493 r_dihedral_angle_4_deg 15.412 r_dihedral_angle_3_deg 11.959 r_sphericity_bonded 8.522 r_dihedral_angle_1_deg 5.966 r_rigid_bond_restr 2 r_scbond_it 1.728 r_angle_refined_deg 1.474 r_mcangle_it 1.432
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.49 r_sphericity_free 25.493 r_dihedral_angle_4_deg 15.412 r_dihedral_angle_3_deg 11.959 r_sphericity_bonded 8.522 r_dihedral_angle_1_deg 5.966 r_rigid_bond_restr 2 r_scbond_it 1.728 r_angle_refined_deg 1.474 r_mcangle_it 1.432 r_mcbond_it 1.119 r_chiral_restr 0.099 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12287 Nucleic Acid Atoms Solvent Atoms 1688 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling