4CLM

Structure of Salmonella typhi type I dehydroquinase irreversibly inhibited with a 1,3,4-trihydroxyciclohexane-1-carboxylic acid derivative


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QFEPDB ENTRY 1QFE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.634% PEG 4000, 0.1 M CITRATE-PHOSPHATE PH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.141.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.59α = 90
b = 44.47β = 95.17
c = 84.98γ = 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)2013-03-08MSINGLE 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
11.447.17960.0612.83.685495-39.2
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)
11.41.4876.10.224.12.7

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 1QFE1.447.2181186429395.950.121680.11990.15498RANDOM12.231
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]
0.16-0.470.69-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.369
r_sphericity_free28.717
r_dihedral_angle_4_deg15.135
r_dihedral_angle_3_deg13.353
r_scbond_it8.568
r_sphericity_bonded7.921
r_mcangle_it7.551
r_mcbond_it5.7767
r_dihedral_angle_1_deg5.678
r_scangle_it4.247
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.369
r_sphericity_free28.717
r_dihedral_angle_4_deg15.135
r_dihedral_angle_3_deg13.353
r_scbond_it8.568
r_sphericity_bonded7.921
r_mcangle_it7.551
r_mcbond_it5.7767
r_dihedral_angle_1_deg5.678
r_scangle_it4.247
r_mcbond_other2.2897
r_rigid_bond_restr1.847
r_angle_refined_deg1.533
r_angle_other_deg0.947
r_symmetry_vdw_refined0.287
r_nbd_refined0.284
r_symmetry_hbond_refined0.2645
r_symmetry_vdw_other0.243
r_nbtor_refined0.172
r_nbd_other0.171
r_xyhbond_nbd_refined0.163
r_metal_ion_refined0.151
r_xyhbond_nbd_other0.119
r_chiral_restr0.091
r_nbtor_other0.083
r_symmetry_hbond_other0.071
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
r_metal_ion_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 Atoms3790
Nucleic Acid Atoms
Solvent Atoms665
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEdata scaling
MOLREPphasing