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Structure of Helicobacter pylori Csd3 from the hexagonal crystal
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.9 296 200 mM di-ammonium hydrogen phosphate, pH 7.9, 20% (v/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.65 53.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.469 α = 90 b = 91.469 β = 90 c = 186.963 γ = 120
Symmetry Space Group P 65 2 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 Bruker DIP-6040 hybrid-type of image plates and a CCD 2012-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.98 50 99.9 0.088 0.088 41.917 10.6 31293 -3
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 1.98 2.01 100 0.877 3.519 10.8
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 SAD THROUGHOUT 1.98 50 31293 1672 99.85 0.20903 0.20746 0.2161 0.23858 0.2424 RANDOM 40.639
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] 0.96 0.48 0.96 -3.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.162 r_dihedral_angle_4_deg 17.912 r_dihedral_angle_3_deg 13.984 r_long_range_B_refined 6.683 r_long_range_B_other 6.683 r_dihedral_angle_1_deg 6.051 r_scangle_other 4.69 r_mcangle_it 3.522 r_mcangle_other 3.521 r_scbond_it 2.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.162 r_dihedral_angle_4_deg 17.912 r_dihedral_angle_3_deg 13.984 r_long_range_B_refined 6.683 r_long_range_B_other 6.683 r_dihedral_angle_1_deg 6.051 r_scangle_other 4.69 r_mcangle_it 3.522 r_mcangle_other 3.521 r_scbond_it 2.938 r_scbond_other 2.938 r_mcbond_it 2.398 r_mcbond_other 2.392 r_angle_refined_deg 1.42 r_angle_other_deg 0.736 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2919 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 36
Software Software Software Name Purpose HKL-2000 data collection SOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling