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Crystal structure of Helicobactor pylori shikimate kinase in complex with NSC162535
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZUH PDB ENTRY 1ZUH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 293 0.1M sodium HEPES, 1.2M potassium sodium tartrate tetrahydrate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.91 57.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.91 α = 90 b = 71.791 β = 91.96 c = 47.626 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 193 CCD ADSC QUANTUM 210r 2010-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL12B2 1.0000 SPring-8 BL12B2
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 2.53 30 99.7 0.053 0.053 26.88 5.1 21908 21900 2 2 40
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.53 2.62 98.3 0.305 0.305 4.33 4.7 2150
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1ZUH 2.53 30 20900 20807 1101 99.49 0.21933 0.21703 0.2151 0.26309 0.2211 RANDOM 44.303
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] -3.29 -0.75 -0.41 3.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.328 r_dihedral_angle_4_deg 22.03 r_dihedral_angle_3_deg 21.137 r_dihedral_angle_1_deg 6.501 r_scangle_it 4.99 r_scbond_it 3.047 r_angle_refined_deg 2.018 r_mcangle_it 1.89 r_mcbond_it 0.964 r_chiral_restr 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.328 r_dihedral_angle_4_deg 22.03 r_dihedral_angle_3_deg 21.137 r_dihedral_angle_1_deg 6.501 r_scangle_it 4.99 r_scbond_it 3.047 r_angle_refined_deg 2.018 r_mcangle_it 1.89 r_mcbond_it 0.964 r_chiral_restr 0.136 r_bond_refined_d 0.022 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3661 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 116
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling