3MUF

Shikimate kinase from Helicobacter pylori in complex with shikimate-3-phosphate and ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZUIPDB ENTRY 1ZUI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529318% PEG 8000, 0.1M sodium acetate, 0.1M HEPES, 2% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.2261.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.816α = 90
b = 98.816β = 90
c = 42.129γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray193CCDADSC QUANTUM 315r2010-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13C10.97622NSRRCBL13C1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.33099.90.0680.06829.2811.7105852236
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)RedundancyNumber Unique Reflections (All)
12.32.3899.50.4880.4882.4710.72011

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 REPLACEMENTTHROUGHOUTPDB ENTRY 1ZUI2.33022100031000353799.620.23350.23350.231260.27694RANDOM56.19
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]
-6-3-69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.603
r_dihedral_angle_3_deg21.488
r_dihedral_angle_4_deg20.003
r_dihedral_angle_1_deg7.372
r_scangle_it4.299
r_scbond_it2.649
r_angle_refined_deg1.78
r_mcangle_it1.757
r_mcbond_it0.923
r_chiral_restr0.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.603
r_dihedral_angle_3_deg21.488
r_dihedral_angle_4_deg20.003
r_dihedral_angle_1_deg7.372
r_scangle_it4.299
r_scbond_it2.649
r_angle_refined_deg1.78
r_mcangle_it1.757
r_mcbond_it0.923
r_chiral_restr0.117
r_bond_refined_d0.018
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1279
Nucleic Acid Atoms
Solvent Atoms59
Heterogen Atoms43

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling