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Structure of Cadmium bound KDO8PS from H.pylori
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 3350, HEPES, magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.24 45.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.353 α = 90 b = 51.017 β = 104.7 c = 78.667 γ = 90
Symmetry Space Group C 1 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 315r 2013-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.0 PAL/PLS 5C (4A)
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 1.93 50 92.2 32.85 3.5 36113
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 THROUGHOUT 1.93 28.97 36113 1915 93.08 0.19174 0.19063 0.2032 0.21181 0.2204 RANDOM 24.466
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] 1.58 0.9 -1.02 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.935 r_sphericity_free 29.128 r_dihedral_angle_3_deg 16.247 r_dihedral_angle_4_deg 15.121 r_sphericity_bonded 10.869 r_dihedral_angle_1_deg 6.049 r_rigid_bond_restr 3.275 r_angle_refined_deg 1.362 r_angle_other_deg 1.199 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.935 r_sphericity_free 29.128 r_dihedral_angle_3_deg 16.247 r_dihedral_angle_4_deg 15.121 r_sphericity_bonded 10.869 r_dihedral_angle_1_deg 6.049 r_rigid_bond_restr 3.275 r_angle_refined_deg 1.362 r_angle_other_deg 1.199 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4002 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing