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Structure of a double methionine mutant of NI-FE 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 PEG6000, Glycerol, PH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.6 α = 90 b = 99.9 β = 91.6 c = 183 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 2006-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0 ESRF ID23-1
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 2.4 25 95.3 0.095 0.095 11.8 4.6 90034 86780 42.8
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 2.4 2.5 80.1 0.24 0.24 4.4 2.3 10437
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 2.4 24.99 82430 4350 95.43 0.152 0.15 0.1507 0.194 0.1926 RANDOM 41.66
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] 3.52 0.63 -0.63 -2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.58 r_dihedral_angle_4_deg 15.04 r_dihedral_angle_3_deg 14.421 r_dihedral_angle_1_deg 5.597 r_scangle_it 3.666 r_scbond_it 2.612 r_mcangle_it 1.429 r_angle_refined_deg 1.192 r_mcbond_it 0.969 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.58 r_dihedral_angle_4_deg 15.04 r_dihedral_angle_3_deg 14.421 r_dihedral_angle_1_deg 5.597 r_scangle_it 3.666 r_scbond_it 2.612 r_mcangle_it 1.429 r_angle_refined_deg 1.192 r_mcbond_it 0.969 r_nbtor_refined 0.305 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.204 r_symmetry_vdw_refined 0.193 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.078 r_bond_refined_d 0.01 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 18417 Nucleic Acid Atoms Solvent Atoms 850 Heterogen Atoms 144
Software Software Software Name Purpose AMoRE phasing REFMAC refinement ADSC data collection XDS data reduction XDS data scaling