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Crystal structure of novel carcinogenic factor of H. pylori
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 10% PEG 6000, 5% MPD, 0.1M HEPES (pH 7.5), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.53 51.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.518 α = 90 b = 69.518 β = 90 c = 69.161 γ = 120
Symmetry Space Group P 32 2 1
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 2004-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A Photon Factory BL-5A
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 2.47 50 98.3 0.061 21.3 7 7160 7038 1 70.382
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 2.47 2.6 100 0.133 7.3 1006
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 MIR THROUGHOUT 2.47 45.64 6779 322 98.12 0.22897 0.22641 0.2342 0.2809 0.2992 RANDOM 39.455
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] 2.28 1.14 2.28 -3.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.353 r_scangle_it 3.653 r_scbond_it 2.196 r_angle_refined_deg 1.844 r_mcangle_it 1.342 r_angle_other_deg 0.986 r_mcbond_it 0.725 r_symmetry_hbond_refined 0.319 r_symmetry_vdw_refined 0.253 r_nbd_other 0.238
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.353 r_scangle_it 3.653 r_scbond_it 2.196 r_angle_refined_deg 1.844 r_mcangle_it 1.342 r_angle_other_deg 0.986 r_mcbond_it 0.725 r_symmetry_hbond_refined 0.319 r_symmetry_vdw_refined 0.253 r_nbd_other 0.238 r_symmetry_vdw_other 0.237 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.222 r_chiral_restr 0.125 r_nbtor_other 0.095 r_bond_refined_d 0.019 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 1145 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection SOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling