2ZIZ

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


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
2.4249.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.55α = 90
b = 111.317β = 96.77
c = 94.473γ = 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)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
12.210094.493598242.15
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2670.71

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 3CE62.238.189359893598489994.40.202050.197640.285RANDOM43.792
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]
-0.970.06-1.052.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.031
r_dihedral_angle_4_deg19.999
r_dihedral_angle_3_deg18.096
r_scangle_it9.049
r_scbond_it7.68
r_dihedral_angle_1_deg7.335
r_mcangle_it5.714
r_mcbond_it4.521
r_angle_refined_deg1.873
r_symmetry_hbond_refined0.378
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.031
r_dihedral_angle_4_deg19.999
r_dihedral_angle_3_deg18.096
r_scangle_it9.049
r_scbond_it7.68
r_dihedral_angle_1_deg7.335
r_mcangle_it5.714
r_mcbond_it4.521
r_angle_refined_deg1.873
r_symmetry_hbond_refined0.378
r_nbtor_refined0.307
r_nbd_refined0.226
r_symmetry_vdw_refined0.191
r_xyhbond_nbd_refined0.179
r_chiral_restr0.123
r_bond_refined_d0.019
r_gen_planes_refined0.007
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 Atoms760
Heterogen Atoms252

Software

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