4CNP

Structure of the Salmonella typhi type I dehydroquinase inhibited by a 3-epiquinic acid derivative


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.430% PEG 4000, 0.1 M CITRATE-PHOSPHATE PH 6.4
Crystal Properties
Matthews coefficientSolvent content
2.139.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.216α = 90
b = 44.473β = 95.2
c = 84.702γ = 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)2013-11-08MSINGLE 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
11.1584.3598.60.0512.93.1156242-38.3
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)
11.151.2195.90.333.22.6

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 1QFE1.1551.17153096312498.510.133960.133440.16031RANDOM11.232
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]
0.21-0.25-0.03-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.237
r_sphericity_free22.142
r_dihedral_angle_4_deg14.715
r_dihedral_angle_3_deg12.905
r_scbond_it6.021
r_sphericity_bonded5.697
r_dihedral_angle_1_deg5.695
r_mcangle_it5.096
r_mcbond_it3.724
r_scangle_it2.797
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.237
r_sphericity_free22.142
r_dihedral_angle_4_deg14.715
r_dihedral_angle_3_deg12.905
r_scbond_it6.021
r_sphericity_bonded5.697
r_dihedral_angle_1_deg5.695
r_mcangle_it5.096
r_mcbond_it3.724
r_scangle_it2.797
r_mcbond_other1.494
r_rigid_bond_restr1.358
r_angle_refined_deg1.354
r_angle_other_deg0.784
r_nbd_refined0.244
r_symmetry_vdw_refined0.237
r_symmetry_vdw_other0.206
r_nbtor_refined0.175
r_nbd_other0.171
r_xyhbond_nbd_refined0.138
r_metal_ion_refined0.095
r_nbtor_other0.085
r_symmetry_hbond_refined0.085
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3860
Nucleic Acid Atoms
Solvent Atoms668
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEdata scaling
MOLREPphasing