3DHY

Crystal Structures of Mycobacterium tuberculosis S-Adenosyl-L-Homocysteine Hydrolase in Ternary Complex with Substrate and Inhibitors


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5291.50.2 M MgCl2, 0.1 M Tris pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K
Crystal Properties
Matthews coefficientSolvent content
2.4148.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.2α = 90
b = 111.69β = 96.01
c = 100.13γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC QUANTUM 315mirrors2008-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.979APS19-ID

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
11.299.558.80.309238439522
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)
1.191.233.10.6770.7

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 REPLACEMENTTHROUGHOUT3CE6230114623108886571482.510.264050.260070.34004RANDOM35.22
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]
-1.230.751.87-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.439
r_dihedral_angle_4_deg18.852
r_dihedral_angle_3_deg16.45
r_scangle_it8.206
r_scbond_it6.903
r_dihedral_angle_1_deg6.514
r_mcangle_it5.006
r_mcbond_it3.961
r_angle_refined_deg1.628
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.439
r_dihedral_angle_4_deg18.852
r_dihedral_angle_3_deg16.45
r_scangle_it8.206
r_scbond_it6.903
r_dihedral_angle_1_deg6.514
r_mcangle_it5.006
r_mcbond_it3.961
r_angle_refined_deg1.628
r_nbtor_refined0.309
r_nbd_refined0.218
r_symmetry_vdw_refined0.195
r_xyhbond_nbd_refined0.152
r_symmetry_hbond_refined0.14
r_chiral_restr0.104
r_bond_refined_d0.015
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 Atoms14998
Nucleic Acid Atoms
Solvent Atoms350
Heterogen Atoms260

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
d*TREKdata reduction
d*TREKdata scaling
CCP4phasing