4CNO

Structure of the Salmonella typhi Type I dehydroquinase inhibited by a 3-dehydroquinic acid derivative


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.232% PEG 4000, 0.1 M NA-CITRATE PH 5.2
Crystal Properties
Matthews coefficientSolvent content
2.142.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.67α = 90
b = 39.406β = 104.68
c = 155.13γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MPLANE-ELLIPSOIDAL MIRRORS (SI, RH, IR)2013-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOCALBAXALOC

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
11.5150.0788.40.0414.22.9131130-316.7
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)
11.51.5850.70.322.11.8

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 1QFE1.5150.07124425669088.260.181770.180050.21363RANDOM20.804
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]
-12.530.4216.29-3.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.513
r_dihedral_angle_4_deg17.205
r_dihedral_angle_3_deg13.953
r_dihedral_angle_1_deg5.827
r_scbond_it2.487
r_mcangle_it1.721
r_angle_refined_deg1.276
r_mcbond_it1.099
r_scangle_it0.841
r_angle_other_deg0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.513
r_dihedral_angle_4_deg17.205
r_dihedral_angle_3_deg13.953
r_dihedral_angle_1_deg5.827
r_scbond_it2.487
r_mcangle_it1.721
r_angle_refined_deg1.276
r_mcbond_it1.099
r_scangle_it0.841
r_angle_other_deg0.76
r_symmetry_vdw_refined0.236
r_mcbond_other0.231
r_nbd_refined0.216
r_nbtor_refined0.173
r_symmetry_hbond_refined0.166
r_nbd_other0.165
r_xyhbond_nbd_refined0.139
r_symmetry_vdw_other0.132
r_xyhbond_nbd_other0.122
r_nbtor_other0.083
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
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 Atoms7617
Nucleic Acid Atoms
Solvent Atoms297
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEdata scaling
MOLREPphasing