4FSH

Crystal Structure of Shikimate Dehydrogenase (aroE) Clinical Variant v2356 from Helicobacter pylori in Complex with Shikimate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PHGPDB ENTRY 3PHG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2931.5M ammonium sulfate, 1.0M lithium sulfate, 0.1M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.362.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.118α = 90
b = 71.87β = 90
c = 176.388γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315mirrors2012-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.0000NSRRCBL13B1

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
12.853099.90.072158.219482
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)
12.852.951000.4644.98.51891

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3PHG2.85301932497199.520.21660.21430.26RANDOM67.7202
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]
2.513.74-6.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.211
r_dihedral_angle_4_deg24.916
r_dihedral_angle_3_deg23.778
r_dihedral_angle_1_deg7.603
r_scangle_it4.573
r_scbond_it2.618
r_mcangle_it2.015
r_angle_refined_deg1.312
r_mcbond_it1.031
r_chiral_restr0.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.211
r_dihedral_angle_4_deg24.916
r_dihedral_angle_3_deg23.778
r_dihedral_angle_1_deg7.603
r_scangle_it4.573
r_scbond_it2.618
r_mcangle_it2.015
r_angle_refined_deg1.312
r_mcbond_it1.031
r_chiral_restr0.098
r_bond_refined_d0.017
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4097
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms12

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing