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The crystal structure of the apoenzyme of the iron-sulfur-cluster-free hydrogenase (Hmd)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other In-house Se-MAD model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 283 Hepes/NaOH, 2-propanol, PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.37 47.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.47 α = 90 b = 59.88 β = 90 c = 68.49 γ = 90
Symmetry Space Group P 21 21 2
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 225 mm CCD 2005-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97858 SLS X10SA
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 1.75 40 99.6 0.075 14.1 3.8 38541 38541
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 1.75 1.795 99.8 0.64 2.5 4 2820
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 structure of Hmd from Methanopyrus kandleri 1.75 40 38541 36576 1933 99.59 0.193 0.19146 0.1909 0.21679 0.2047 RANDOM 32.395
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] -1.2 0.09 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.716 r_dihedral_angle_4_deg 23.446 r_dihedral_angle_3_deg 17.206 r_dihedral_angle_1_deg 5.059 r_scangle_it 3.995 r_scbond_it 2.558 r_angle_refined_deg 1.54 r_mcangle_it 1.411 r_mcbond_it 0.959 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.716 r_dihedral_angle_4_deg 23.446 r_dihedral_angle_3_deg 17.206 r_dihedral_angle_1_deg 5.059 r_scangle_it 3.995 r_scbond_it 2.558 r_angle_refined_deg 1.54 r_mcangle_it 1.411 r_mcbond_it 0.959 r_nbtor_refined 0.312 r_nbd_refined 0.23 r_symmetry_vdw_refined 0.199 r_xyhbond_nbd_refined 0.14 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2593 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling EPMR phasing