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H. pylori type II DHQase in complex with citrate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 295 PEG 4000, SODIUM CHOLRIDE, SODIUM CITRATE, EDTA, 2-MERCAPTOETHANOL, PH 5.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K
Crystal Properties Matthews coefficient Solvent content 2.3 46.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.91 α = 90 b = 98.91 β = 90 c = 98.91 γ = 90
Symmetry Space Group P 42 3 2
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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A Photon Factory BL-6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.5 44 100 0.09 38 6146 53.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 100 0.48
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION OTHER THROUGHOUT 2.5 30 5726 311 98.2 0.172 0.17 0.212 RANDOM 38.82
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.942 r_dihedral_angle_3_deg 20.176 r_dihedral_angle_4_deg 18.708 r_dihedral_angle_1_deg 8.049 r_scangle_it 3.805 r_scbond_it 2.605 r_angle_refined_deg 2.24 r_angle_other_deg 1.933 r_mcangle_it 1.817 r_mcbond_it 1.485
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.942 r_dihedral_angle_3_deg 20.176 r_dihedral_angle_4_deg 18.708 r_dihedral_angle_1_deg 8.049 r_scangle_it 3.805 r_scbond_it 2.605 r_angle_refined_deg 2.24 r_angle_other_deg 1.933 r_mcangle_it 1.817 r_mcbond_it 1.485 r_symmetry_vdw_refined 0.272 r_xyhbond_nbd_refined 0.242 r_nbd_refined 0.228 r_nbd_other 0.208 r_symmetry_vdw_other 0.207 r_symmetry_hbond_refined 0.199 r_nbtor_refined 0.192 r_chiral_restr 0.129 r_nbtor_other 0.103 r_bond_refined_d 0.027 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1221 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling