2XD9

STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR COMPOUND (4R,6R,7S)-4,6,7-Trihydroxy-2-((E)-prop-1- enyl)-4,5,6,7-tetrahydrobenzo(b)thiophene-4-carboxylic acid


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.850 MM TRIS-HCL PH 7.5 1 MM 2-MERCAPTOETHANOL 1 MM ETHYLENEDIAMINETETRAACETIC ACID 200 MM SODIUM CHLORIDE 24% (W/V) POLYETHYLENEGLYCOL 4000 100 MM SODIUM CITRATE, PH 5.8 12.5 MM (4R, 6R, 7S)-4,6, 7-TRIHYDROXY-2-[(E)-PROP-1-ENYL]-4,5,6, 7-TETRAHYDROBENZO[B]THIOPHENE-4-CARBOXYLIC ACID 0.13 % (V/V) METHANOL
Crystal Properties
Matthews coefficientSolvent content
2.3547.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.217α = 90
b = 100.217β = 90
c = 103.934γ = 90
Symmetry
Space GroupP 42 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
11.953498.70.085.812.53862624.2
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)
11.952.0699.70.361.812.1

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 2C4V1.951536894153699.550.212180.21050.25025THIN SHELLS25.237
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]
-0.75-0.751.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.521
r_dihedral_angle_3_deg15.433
r_dihedral_angle_4_deg8.672
r_dihedral_angle_1_deg5.752
r_scangle_it3.262
r_scbond_it2.143
r_mcangle_it1.717
r_angle_refined_deg1.449
r_mcbond_it0.973
r_angle_other_deg0.894
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.521
r_dihedral_angle_3_deg15.433
r_dihedral_angle_4_deg8.672
r_dihedral_angle_1_deg5.752
r_scangle_it3.262
r_scbond_it2.143
r_mcangle_it1.717
r_angle_refined_deg1.449
r_mcbond_it0.973
r_angle_other_deg0.894
r_nbd_refined0.212
r_symmetry_vdw_refined0.205
r_mcbond_other0.189
r_xyhbond_nbd_refined0.182
r_nbd_other0.181
r_nbtor_refined0.176
r_symmetry_hbond_refined0.155
r_symmetry_vdw_other0.144
r_chiral_restr0.09
r_nbtor_other0.086
r_xyhbond_nbd_other0.017
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms3528
Nucleic Acid Atoms
Solvent Atoms286
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing