2RIJ

Crystal structure of a putative 2,3,4,5-tetrahydropyridine-2-carboxylate n-succinyltransferase (cj1605c, dapd) from campylobacter jejuni at 1.90 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5277NANODROP, 1.0M Na Citrate, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
4.3871.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.093α = 90
b = 135.093β = 90
c = 213.742γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDAdjustable focusing mirrors in K-B geometry2007-08-19MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.97957, 0.95373, 0.97942APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.929.541000.1240.1244.17.55912126.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.951000.0111.0680.77.54335

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.929.545911929911000.1570.1560.185RANDOM21.932
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]
1.280.641.28-1.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.637
r_dihedral_angle_4_deg18.951
r_dihedral_angle_3_deg12.095
r_scangle_it7.341
r_dihedral_angle_1_deg5.982
r_scbond_it5.439
r_mcangle_it3.005
r_mcbond_it2.274
r_angle_refined_deg1.55
r_angle_other_deg0.953
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.637
r_dihedral_angle_4_deg18.951
r_dihedral_angle_3_deg12.095
r_scangle_it7.341
r_dihedral_angle_1_deg5.982
r_scbond_it5.439
r_mcangle_it3.005
r_mcbond_it2.274
r_angle_refined_deg1.55
r_angle_other_deg0.953
r_mcbond_other0.567
r_symmetry_vdw_other0.278
r_symmetry_vdw_refined0.232
r_symmetry_hbond_refined0.222
r_nbd_refined0.196
r_nbd_other0.187
r_nbtor_refined0.176
r_xyhbond_nbd_refined0.155
r_chiral_restr0.096
r_nbtor_other0.084
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2904
Nucleic Acid Atoms
Solvent Atoms448
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
SHELXDphasing
SHARPphasing