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X-ray structure of the FeFe-hydrogenase maturase HydE from T. maritima in complex with methionine and 5'deoxyadenosine
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 8.5 294 PEG 4000, LiSO4, TRIS pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.18 43.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.054 α = 90 b = 78.925 β = 90 c = 86.192 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 315r 2008-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.25 58.22 95.1 0.045 14.87 3.2 88534 15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.25 1.33 76.8 0.407 2.1 1.46 31571
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 1.25 58.22 88534 4675 96.45 0.13996 0.13857 0.1369 0.16623 0.1662 RANDOM 11.993
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] 0.78 -0.04 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.744 r_dihedral_angle_1_deg 18.802 r_dihedral_angle_4_deg 15.557 r_dihedral_angle_3_deg 12.431 r_sphericity_free 5.033 r_scangle_it 3.156 r_sphericity_bonded 2.594 r_scbond_it 2.366 r_mcangle_it 1.73 r_angle_refined_deg 1.675
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.744 r_dihedral_angle_1_deg 18.802 r_dihedral_angle_4_deg 15.557 r_dihedral_angle_3_deg 12.431 r_sphericity_free 5.033 r_scangle_it 3.156 r_sphericity_bonded 2.594 r_scbond_it 2.366 r_mcangle_it 1.73 r_angle_refined_deg 1.675 r_rigid_bond_restr 1.365 r_angle_other_deg 1.256 r_mcbond_it 1.234 r_mcbond_other 0.498 r_nbd_refined 0.254 r_symmetry_vdw_other 0.243 r_nbd_other 0.205 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.179 r_symmetry_hbond_refined 0.164 r_chiral_restr 0.146 r_symmetry_vdw_refined 0.087 r_nbtor_other 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2877 Nucleic Acid Atoms Solvent Atoms 467 Heterogen Atoms 200
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling