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3-D X-Ray structure of the sulfide:quinone oxidoreductase from the hyperthermophilic bacterium Aquifex aeolicus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 4% PEG 400 (V/V), 0.1M NA-MES (SODIUM 2-(N-MORPHOLINO)-ETHANESULFONATE), 2M AMMONIUM SULFATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.73 54.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.85 α = 90 b = 154.92 β = 90 c = 178.04 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 2008-02-24 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL PSI PILATUS 6M dynamically bendable mirror 2008-02-24 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.91984 SLS X10SA 2 SYNCHROTRON SLS BEAMLINE X06SA 1.14000, 1.14050, 1.13010, 1.03864 SLS X06SA
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 2.3 50 97.9 14.87 3.47 135807
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2.3 2.4 87.9 3.44 2.47
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MIRAS THROUGHOUT 2.3 20.04 128783 6821 97.94 0.19534 0.19321 0.2167 0.23537 0.257 RANDOM 38.517
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] 1.32 -0.09 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.217 r_dihedral_angle_4_deg 20.052 r_dihedral_angle_3_deg 15.77 r_dihedral_angle_1_deg 5.351 r_scangle_it 1.654 r_angle_refined_deg 1.254 r_scbond_it 1.043 r_mcangle_it 0.648 r_mcbond_it 0.412 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.217 r_dihedral_angle_4_deg 20.052 r_dihedral_angle_3_deg 15.77 r_dihedral_angle_1_deg 5.351 r_scangle_it 1.654 r_angle_refined_deg 1.254 r_scbond_it 1.043 r_mcangle_it 0.648 r_mcbond_it 0.412 r_nbtor_refined 0.303 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.132 r_xyhbond_nbd_refined 0.119 r_symmetry_hbond_refined 0.088 r_chiral_restr 0.08 r_bond_refined_d 0.01 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 20016 Nucleic Acid Atoms Solvent Atoms 571 Heterogen Atoms 768
Software Software Software Name Purpose XDS data scaling SHARP phasing REFMAC refinement XDS data reduction XSCALE data scaling