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Structure of the T18G small subunit mutant of D. fructosovorans NiFe- hydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YQW PDB ENTRY 1YQW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 VAPOR DIFFUSION, PH 6.0, 293 K, PEG 6000, MES, IN A GLOVEBOX
Crystal Properties Matthews coefficient Solvent content 2.1 41.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.6 α = 90 b = 99.27 β = 92.32 c = 182.08 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 293 PIXEL DECTRIS PILATUS 2012-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 1.95 50 99.2 0.04 13.6 3.3 160613
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 1.95 2.01 99.3 0.37 2.3 3.3
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 1YQW 1.95 25 152472 8066 99.17 0.19843 0.19676 0.2183 0.23068 0.2497 RANDOM 40.912
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] 5.02 2.23 -1.31 -3.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.664 r_dihedral_angle_4_deg 17.134 r_dihedral_angle_3_deg 13.857 r_dihedral_angle_1_deg 5.982 r_scangle_it 4.398 r_scbond_it 3.492 r_mcangle_it 2.099 r_mcbond_it 1.492 r_angle_refined_deg 1.351 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.664 r_dihedral_angle_4_deg 17.134 r_dihedral_angle_3_deg 13.857 r_dihedral_angle_1_deg 5.982 r_scangle_it 4.398 r_scbond_it 3.492 r_mcangle_it 2.099 r_mcbond_it 1.492 r_angle_refined_deg 1.351 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18362 Nucleic Acid Atoms Solvent Atoms 606 Heterogen Atoms 151
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing