3CE6

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LI4PDB ENTRY 1LI4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18291.520% PEG 1000, 200 mM Imidazole pH 8.0, 100 mM Calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K
Crystal Properties
Matthews coefficientSolvent content
2.5151.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.04α = 90
b = 112.133β = 92.41
c = 100.234γ = 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-IDAPS19-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
11.510094.90.04870.048713.1308888217
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)
11.51.5473.40.68210.68211.48

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 1LI41.6303088882734641379597.10.2020.20.238RANDOM18.37
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]
1.520.31-1.09-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.095
r_dihedral_angle_4_deg19.471
r_dihedral_angle_3_deg13.642
r_scangle_it7.496
r_dihedral_angle_1_deg6.531
r_scbond_it5.82
r_mcangle_it3.811
r_mcbond_it3.175
r_angle_refined_deg2.394
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.095
r_dihedral_angle_4_deg19.471
r_dihedral_angle_3_deg13.642
r_scangle_it7.496
r_dihedral_angle_1_deg6.531
r_scbond_it5.82
r_mcangle_it3.811
r_mcbond_it3.175
r_angle_refined_deg2.394
r_nbtor_refined0.311
r_symmetry_vdw_refined0.244
r_nbd_refined0.232
r_chiral_restr0.203
r_xyhbond_nbd_refined0.166
r_symmetry_hbond_refined0.141
r_bond_refined_d0.031
r_gen_planes_refined0.014
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 Atoms1736
Heterogen Atoms252

Software

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