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Crystal structure of the catalytic domain of cholesterol-alpha-glucosyltransferase from Helicobacter pylori
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 297 0.1M HEPES (pH 7.5), 25% (w/v) PEG 3350, 0.1M glycine, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.06 40.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.786 α = 101.44 b = 40.714 β = 94.87 c = 53.738 γ = 90.58
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 315 2008-11-23 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2008-11-28 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A 2 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.9194, 0.9196, 0.9062 Photon Factory BL-5A
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 1.5 20 96 45557
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 1.5 1.53 94.3 0.141 0.138 8.6 3.1
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 MAD THROUGHOUT 1.5 19.94 43082 2306 95.95 0.19757 0.196 0.1946 0.22734 0.2263 RANDOM 17.49
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] 0.1 0.12 -0.27 -0.11 -0.62 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.658 r_dihedral_angle_4_deg 16.81 r_dihedral_angle_3_deg 12.615 r_dihedral_angle_1_deg 6.577 r_scangle_it 3.408 r_scbond_it 2.012 r_mcangle_it 1.413 r_angle_refined_deg 1.315 r_mcbond_it 0.766 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.658 r_dihedral_angle_4_deg 16.81 r_dihedral_angle_3_deg 12.615 r_dihedral_angle_1_deg 6.577 r_scangle_it 3.408 r_scbond_it 2.012 r_mcangle_it 1.413 r_angle_refined_deg 1.315 r_mcbond_it 0.766 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 2440 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection SOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling