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X-ray structure of the FeFe-hydrogenase maturase HydE from T. maritima in complex with S-adenosyl-L-methionine
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 2.15 42.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.628 α = 90 b = 78.78 β = 90 c = 85.943 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 2005-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 1.62 43 93.5 0.066 13.39 2.5 41143 14
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) 1.62 1.72 72.9 0.369 2.38 1.45 13887
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 1.62 38.16 41143 2204 97.58 0.1399 0.13754 0.1485 0.18438 0.1884 RANDOM 12.188
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] 0.62 0.06 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.806 r_dihedral_angle_4_deg 15.901 r_dihedral_angle_3_deg 12.335 r_dihedral_angle_1_deg 11.92 r_sphericity_free 5.306 r_scangle_it 3.374 r_scbond_it 2.496 r_sphericity_bonded 2.43 r_angle_refined_deg 1.749 r_mcangle_it 1.616
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.806 r_dihedral_angle_4_deg 15.901 r_dihedral_angle_3_deg 12.335 r_dihedral_angle_1_deg 11.92 r_sphericity_free 5.306 r_scangle_it 3.374 r_scbond_it 2.496 r_sphericity_bonded 2.43 r_angle_refined_deg 1.749 r_mcangle_it 1.616 r_rigid_bond_restr 1.598 r_mcbond_it 1.175 r_angle_other_deg 0.954 r_mcbond_other 0.424 r_nbd_refined 0.251 r_symmetry_vdw_other 0.243 r_nbd_other 0.211 r_symmetry_hbond_refined 0.208 r_xyhbond_nbd_refined 0.205 r_nbtor_refined 0.179 r_chiral_restr 0.099 r_symmetry_vdw_refined 0.098 r_nbtor_other 0.085 r_xyhbond_nbd_other 0.016 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2822 Nucleic Acid Atoms Solvent Atoms 446 Heterogen Atoms 198
Software Software Software Name Purpose ProDC data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing