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3-D X-Ray structure of the sulfide:quinone oxidoreductase of the hyperthermophilic bacterium Aquifex aeolicus in complex with decylubiquinone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H27 PDB ENTRY 3H27
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 4% PEG 400, 2M AMMONIUM SULFATE, 0.1M NA-ACETATE, PH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.62 53.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.78 α = 90 b = 154.01 β = 90 c = 175.55 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 MARMOSAIC 225 mm CCD DYNAMICALLY BENDABLE MIRROR 2008-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00150 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 96.2 13.17 4.74 194489
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.1 76.7 1.86 1.86
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 3H27 2 20.45 184559 9757 96.22 0.20152 0.19972 0.2276 0.2357 0.2576 RANDOM 35.976
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] 0.87 -0.74 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.295 r_dihedral_angle_4_deg 18.421 r_dihedral_angle_3_deg 14.453 r_dihedral_angle_1_deg 5.361 r_scangle_it 1.628 r_angle_refined_deg 1.151 r_scbond_it 1.04 r_mcangle_it 0.654 r_mcbond_it 0.424 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.295 r_dihedral_angle_4_deg 18.421 r_dihedral_angle_3_deg 14.453 r_dihedral_angle_1_deg 5.361 r_scangle_it 1.628 r_angle_refined_deg 1.151 r_scbond_it 1.04 r_mcangle_it 0.654 r_mcbond_it 0.424 r_nbtor_refined 0.307 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.185 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.117 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 20036 Nucleic Acid Atoms Solvent Atoms 1137 Heterogen Atoms 829
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing