☰ Navigation Tabs
Structural Basis for Shikimate-binding Specificity of Helicobacter pylori Shikimate Kinase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Lithium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.6 65.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.286 α = 90 b = 97.286 β = 90 c = 46.909 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2004-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 2.3 84.51 99.7 0.093 11460 11417 1 1
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 2.3 2.38 97.9 97.9 0.451
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MOLECULAR REPLACEMENT THROUGHOUT 2.3 30 2 11460 10842 548 99.56 0.207 0.207 0.203 0.2038 0.28 0.2751 RANDOM 50.345
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] -4.82 -2.41 -4.82 7.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 10.268 r_scangle_it 8.113 r_scbond_it 5.479 r_angle_refined_deg 3.25 r_mcangle_it 3.018 r_mcbond_it 1.626 r_nbd_refined 0.299 r_symmetry_vdw_refined 0.254 r_chiral_restr 0.243 r_xyhbond_nbd_refined 0.213
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 10.268 r_scangle_it 8.113 r_scbond_it 5.479 r_angle_refined_deg 3.25 r_mcangle_it 3.018 r_mcbond_it 1.626 r_nbd_refined 0.299 r_symmetry_vdw_refined 0.254 r_chiral_restr 0.243 r_xyhbond_nbd_refined 0.213 r_bond_refined_d 0.042 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_refined 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 1261 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 17
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction