3PHH

Shikimate 5-Dehydrogenase (aroE) from Helicobacter pylori in complex with Shikimate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529330% PEG 8000, 0.1M BIS-TRIS, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.141.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.37α = 90
b = 62.798β = 90
c = 84.38γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315r2008-12-05MSINGLE 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)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
11.423099.80.0540.05433.874706711
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)
11.421.4798.60.4670.4674.16.74566

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 3PHG1.4224.854713344685238299.830.198840.19730.22728RANDOM16.377
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]
0.050.48-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.054
r_dihedral_angle_3_deg10.661
r_dihedral_angle_4_deg6.751
r_dihedral_angle_1_deg3.597
r_scangle_it3.514
r_scbond_it2.16
r_angle_refined_deg1.419
r_mcangle_it1.309
r_mcbond_it0.681
r_chiral_restr0.063
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.054
r_dihedral_angle_3_deg10.661
r_dihedral_angle_4_deg6.751
r_dihedral_angle_1_deg3.597
r_scangle_it3.514
r_scbond_it2.16
r_angle_refined_deg1.419
r_mcangle_it1.309
r_mcbond_it0.681
r_chiral_restr0.063
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
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 Atoms2038
Nucleic Acid Atoms
Solvent Atoms375
Heterogen Atoms12

Software

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