1ZUI

Structural Basis for Shikimate-binding Specificity of Helicobacter pylori Shikimate Kinase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293Lithium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.665.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.286α = 90
b = 97.286β = 90
c = 46.909γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2004-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.384.5199.70.093114601141711
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3897.997.90.451

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.3302114601084254899.560.2070.2070.2030.28RANDOM50.345
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]
-4.82-2.41-4.827.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg10.268
r_scangle_it8.113
r_scbond_it5.479
r_angle_refined_deg3.25
r_mcangle_it3.018
r_mcbond_it1.626
r_nbd_refined0.299
r_symmetry_vdw_refined0.254
r_chiral_restr0.243
r_xyhbond_nbd_refined0.213
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg10.268
r_scangle_it8.113
r_scbond_it5.479
r_angle_refined_deg3.25
r_mcangle_it3.018
r_mcbond_it1.626
r_nbd_refined0.299
r_symmetry_vdw_refined0.254
r_chiral_restr0.243
r_xyhbond_nbd_refined0.213
r_bond_refined_d0.042
r_gen_planes_refined0.015
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 AtomsNumber
Protein Atoms1261
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms17

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction