2ZJ1

Crystal structure of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with NAD and 3'-keto-aristeromycin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CE6PDB entry 3CE6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8291.520% PEG 1000, 200 mM Imidazole pH 8.0, 100 mM Calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K
Crystal Properties
Matthews coefficientSolvent content
2.4449.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.854α = 90
b = 111.85β = 96.49
c = 100.403γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC QUANTUM 315Mirrors2005-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.96400APS19-ID

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
12.0110098.860.06710.067110.12136379129513225.64
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)
12.012.0689.410.3530.353

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3CE62.0134.59129513129513685398.860.192490.189610.2468RANDOM27.473
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]
2.17-0.19-1.17-1.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.003
r_dihedral_angle_4_deg19.144
r_dihedral_angle_3_deg14.915
r_scangle_it7.57
r_dihedral_angle_1_deg6.542
r_scbond_it5.854
r_mcangle_it4.086
r_mcbond_it3.318
r_angle_refined_deg1.568
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.003
r_dihedral_angle_4_deg19.144
r_dihedral_angle_3_deg14.915
r_scangle_it7.57
r_dihedral_angle_1_deg6.542
r_scbond_it5.854
r_mcangle_it4.086
r_mcbond_it3.318
r_angle_refined_deg1.568
r_nbtor_refined0.297
r_symmetry_vdw_refined0.249
r_nbd_refined0.199
r_symmetry_hbond_refined0.188
r_xyhbond_nbd_refined0.141
r_chiral_restr0.102
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14992
Nucleic Acid Atoms
Solvent Atoms844
Heterogen Atoms252

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing