3ASB

Crystal structure of PLP-bound LL-diaminopimelate aminotransferase from Chlamydia trachomatis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529810% PEG6000, 2.0M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties
Matthew coefficientSolvent content
3.4964.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.486α = 90
b = 110.486β = 90
c = 204.242γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2010-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.7400.05335.88.117651
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.80.6753.38.21733

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.7401670690099.080.225210.222230.28699RANDOM79.91
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]
-1-12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.706
r_dihedral_angle_3_deg22.438
r_dihedral_angle_4_deg18.632
r_dihedral_angle_1_deg8.161
r_scangle_it4.437
r_scbond_it2.656
r_angle_refined_deg2.087
r_mcangle_it1.934
r_mcbond_it1.013
r_chiral_restr0.137
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.706
r_dihedral_angle_3_deg22.438
r_dihedral_angle_4_deg18.632
r_dihedral_angle_1_deg8.161
r_scangle_it4.437
r_scbond_it2.656
r_angle_refined_deg2.087
r_mcangle_it1.934
r_mcbond_it1.013
r_chiral_restr0.137
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_bond_other_d
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_bonded
r_mcbond_other
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2863
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms24

Software

Software
Software NamePurpose
MXDSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling