3JS3

Crystal structure of type I 3-dehydroquinate dehydratase (aroD) from Clostridium difficile with covalent reaction intermediate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7295Protein solution: 7.5mg/mL, 0.25M NaCl, 1mM 3-dehydroshikimate, Tris-HCl pH 8.3. Screen solution: 0.2M Magnesium chloride, 0.1M Tris-HCl pH 7.0, 10% w/v PEG 8000 , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.4149.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.472α = 90
b = 139.619β = 90.63
c = 66.774γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDDiamond2009-08-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
12.23099.90.06617.33.85593855938-344.6
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)
12.22.241000.6142.23.82854

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1QFE2.229.555306853068283999.760.191610.191610.188890.24147RANDOM21.947
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]
0.28-0.211.3-1.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.985
r_dihedral_angle_4_deg12.843
r_dihedral_angle_3_deg11.071
r_scangle_it4.556
r_scbond_it3.038
r_dihedral_angle_1_deg2.732
r_mcangle_it1.758
r_angle_refined_deg1.537
r_mcbond_it0.962
r_angle_other_deg0.904
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.985
r_dihedral_angle_4_deg12.843
r_dihedral_angle_3_deg11.071
r_scangle_it4.556
r_scbond_it3.038
r_dihedral_angle_1_deg2.732
r_mcangle_it1.758
r_angle_refined_deg1.537
r_mcbond_it0.962
r_angle_other_deg0.904
r_mcbond_other0.267
r_chiral_restr0.094
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8032
Nucleic Acid Atoms
Solvent Atoms318
Heterogen Atoms44

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling