2XB9

Structure of Helicobacter pylori type II dehydroquinase in complex with inhibitor compound (2R)-2-(4-methoxybenzyl)-3-dehydroquinic acid


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1520 MG/ML DEHYDROQUINASE; 12.5 MM 2R)-2-(4-METHOXYBENZYL)-3-DEHYDROQUINIC ACID, 50 MM TRIS-HCL PH 7.5, 1 MM 2-MERCAPTOETHANOL, 1 MM ETHYLENEDIAMINETETRAACETIC ACID, 200 MM SODIUM CHLORIDE; 31% (W/V) POLYETHYLENEGLYCOL 4000, 0.1 M SODIUM CITRATE PH 5.0
Crystal Properties
Matthews coefficientSolvent content
2.449

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.56α = 90
b = 100.56β = 90
c = 105.449γ = 90
Symmetry
Space GroupP 42 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295CCDENRAF-NONIUS KAPPA CCD-2000CONFOCAL MULTILAYER GRADED MIRRORS2009-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR591

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
12.753599.90.0422.683.61462961.5
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)
12.752.8599.90.322.393.2

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 2C4V2.7534.221384474899.750.18870.185080.25033RANDOM38.463
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]
-0.72-0.721.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.532
r_dihedral_angle_3_deg16.367
r_dihedral_angle_4_deg11.513
r_dihedral_angle_1_deg6.71
r_scangle_it3.117
r_scbond_it1.772
r_mcangle_it1.667
r_angle_refined_deg1.406
r_mcbond_it0.892
r_angle_other_deg0.889
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.532
r_dihedral_angle_3_deg16.367
r_dihedral_angle_4_deg11.513
r_dihedral_angle_1_deg6.71
r_scangle_it3.117
r_scbond_it1.772
r_mcangle_it1.667
r_angle_refined_deg1.406
r_mcbond_it0.892
r_angle_other_deg0.889
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.18
r_symmetry_vdw_other0.164
r_symmetry_hbond_refined0.136
r_symmetry_vdw_refined0.129
r_mcbond_other0.098
r_nbtor_other0.087
r_chiral_restr0.077
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_nbd_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3663
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing