2ZJ0

Crystal structure of Mycobacterium tuberculosis S-Adenosyl-L-homocysteine hydrolase in ternary complex with NAD and 2-fluoroadenosine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5291.50.2 M Magnesium chloride, 0.1 M Tris-HCl pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K
Crystal Properties
Matthews coefficientSolvent content
2.4950.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.254α = 90
b = 112.079β = 95.15
c = 100.451γ = 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
12.4210091.90.08090.080910.527418770373235.92
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)
12.422.4979.540.4060.406

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 3CE62.4233.157037370373372891.910.198040.193730.27993RANDOM38.276
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]
2.490.33-1.09-1.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.614
r_dihedral_angle_4_deg20.108
r_dihedral_angle_3_deg17.656
r_dihedral_angle_1_deg7.01
r_scangle_it3.074
r_scbond_it1.967
r_angle_refined_deg1.699
r_mcangle_it1.204
r_mcbond_it0.702
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.614
r_dihedral_angle_4_deg20.108
r_dihedral_angle_3_deg17.656
r_dihedral_angle_1_deg7.01
r_scangle_it3.074
r_scbond_it1.967
r_angle_refined_deg1.699
r_mcangle_it1.204
r_mcbond_it0.702
r_nbtor_refined0.306
r_symmetry_hbond_refined0.27
r_nbd_refined0.242
r_symmetry_vdw_refined0.194
r_xyhbond_nbd_refined0.168
r_chiral_restr0.108
r_bond_refined_d0.016
r_gen_planes_refined0.005
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 Atoms14996
Nucleic Acid Atoms
Solvent Atoms711
Heterogen Atoms256

Software

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