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Structure of a double ILE/PHE mutant of NI-FE hydrogenase refined at 2.2 angstrom resolution
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 PEG6000, GLYCEROL, PH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.09 41.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.4 α = 90 b = 99.96 β = 92.23 c = 182.69 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 MIRRORS 2008-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.934 ESRF ID14-4
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 2.18 20 93.3 0.07 0.07 7.2 2.6 115860 108157 27
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 2.18 2.3 71 0.198 0.198 3.3 2.2 17163
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 2.2 20 101754 5404 94.24 0.18677 0.18493 0.2172 0.22223 0.2512 RANDOM 15.032
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] 3.07 0.21 -0.93 -2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.162 r_dihedral_angle_4_deg 14.543 r_dihedral_angle_3_deg 14.12 r_dihedral_angle_1_deg 9.521 r_angle_refined_deg 1.266 r_scangle_it 1.094 r_scbond_it 0.72 r_mcangle_it 0.602 r_mcbond_it 0.401 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.162 r_dihedral_angle_4_deg 14.543 r_dihedral_angle_3_deg 14.12 r_dihedral_angle_1_deg 9.521 r_angle_refined_deg 1.266 r_scangle_it 1.094 r_scbond_it 0.72 r_mcangle_it 0.602 r_mcbond_it 0.401 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.215 r_symmetry_hbond_refined 0.21 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18418 Nucleic Acid Atoms Solvent Atoms 1013 Heterogen Atoms 126
Software Software Software Name Purpose AMoRE phasing REFMAC refinement ADSC data collection XDS data reduction XDS data scaling