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Structure of apo form 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 2.12 41.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.829 α = 90 b = 50.657 β = 110.51 c = 78.67 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 MARMOSAIC 225 mm CCD 2012-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 30 99 46.45 4.9 32093
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 2 30 32093 1702 97.5 0.18955 0.1869 0.1926 0.23915 0.2439 RANDOM 22.538
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] 0.05 -0.02 -0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.71 r_dihedral_angle_4_deg 18.097 r_dihedral_angle_3_deg 14.424 r_dihedral_angle_1_deg 5.873 r_long_range_B_refined 5.675 r_long_range_B_other 5.452 r_scangle_other 3.042 r_mcangle_it 2.422 r_mcangle_other 2.422 r_scbond_it 1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.71 r_dihedral_angle_4_deg 18.097 r_dihedral_angle_3_deg 14.424 r_dihedral_angle_1_deg 5.873 r_long_range_B_refined 5.675 r_long_range_B_other 5.452 r_scangle_other 3.042 r_mcangle_it 2.422 r_mcangle_other 2.422 r_scbond_it 1.83 r_scbond_other 1.83 r_mcbond_it 1.44 r_mcbond_other 1.437 r_angle_refined_deg 1.27 r_angle_other_deg 0.773 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 4033 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing