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X-RAY structure of the [FeFe]-hydrogenase maturase HydE from thermotoga maritima in complex with thiocyanate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CIW PDB ENTRY 3CIW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 PEG4000 35%, 100mM TrisHCl, pH8.5, 100mM LiSO4, 3mM CHAPS, 20mg/mL Protein, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 43.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.927 α = 90 b = 79.728 β = 90 c = 86.077 γ = 90
Symmetry Space Group P 21 21 21
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 4 2006-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.933 ESRF ID14-1
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 1.7 58.52 95.8 0.076 15.9 6.6 37499 17.9
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 1.7 1.79 77.4 0.413 3.4 5.2 4270
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 3CIW 1.7 32.87 35563 1893 95.35 0.14834 0.1462 0.1534 0.18865 0.194 RANDOM 13.913
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] 0.92 0.02 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.602 r_dihedral_angle_4_deg 13.636 r_dihedral_angle_1_deg 12.242 r_dihedral_angle_3_deg 11.999 r_sphericity_free 5.854 r_scangle_it 3.541 r_scbond_it 2.5 r_sphericity_bonded 2.482 r_rigid_bond_restr 2.137 r_angle_refined_deg 1.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.602 r_dihedral_angle_4_deg 13.636 r_dihedral_angle_1_deg 12.242 r_dihedral_angle_3_deg 11.999 r_sphericity_free 5.854 r_scangle_it 3.541 r_scbond_it 2.5 r_sphericity_bonded 2.482 r_rigid_bond_restr 2.137 r_angle_refined_deg 1.746 r_mcangle_it 1.65 r_mcbond_it 1.2 r_angle_other_deg 0.998 r_mcbond_other 0.462 r_symmetry_vdw_refined 0.313 r_symmetry_vdw_other 0.25 r_nbd_refined 0.216 r_nbd_other 0.207 r_symmetry_hbond_refined 0.2 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.173 r_chiral_restr 0.114 r_nbtor_other 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2731 Nucleic Acid Atoms Solvent Atoms 366 Heterogen Atoms 209
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling