5Y8I

Mycobacterium tuberculosis 3-Hydroxyisobutyrate dehydrogenase (MtHIBADH) + (S)-3-hydroxyisobutyrate (S-HIBA)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH7.52950.02M MgCl2.6H2O, 0.1M HEPES pH 7.5, 22% w/v polyacrylic acid sodium salt 5100
Crystal Properties
Matthews coefficientSolvent content
2.8456.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.58α = 90
b = 128.58β = 90
c = 70.23γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2015-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
12.04111.3598.28.17.941507
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)
12.042.1598.20.1778.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3OBB2.04111.3539336209898.10.1680.1660.207RANDOM24.57
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]
-0.05-0.03-0.050.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.379
r_dihedral_angle_4_deg15.435
r_dihedral_angle_3_deg13.403
r_long_range_B_refined6.323
r_long_range_B_other6.323
r_dihedral_angle_1_deg5.794
r_scangle_other2.87
r_scbond_it1.772
r_scbond_other1.771
r_mcangle_other1.753
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.379
r_dihedral_angle_4_deg15.435
r_dihedral_angle_3_deg13.403
r_long_range_B_refined6.323
r_long_range_B_other6.323
r_dihedral_angle_1_deg5.794
r_scangle_other2.87
r_scbond_it1.772
r_scbond_other1.771
r_mcangle_other1.753
r_mcangle_it1.75
r_angle_refined_deg1.346
r_mcbond_it1.071
r_mcbond_other1.066
r_angle_other_deg0.971
r_chiral_restr0.08
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4105
Nucleic Acid Atoms
Solvent Atoms611
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing