5Y8H

Mycobacterium tuberculosis 3-Hydroxyisobutyrate dehydrogenase (MtHIBADH) + NAD+


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
2.8356.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.43α = 90
b = 129.43β = 90
c = 70.49γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2015-09-29MSINGLE 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
12.1112.0998.69.58.938867

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 REPLACEMENTTHROUGHOUT3OBB2.1112.0936791195598.340.161970.159420.21066RANDOM25.426
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]
0.190.10.19-0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.629
r_dihedral_angle_4_deg15.913
r_dihedral_angle_3_deg13.18
r_long_range_B_refined8.129
r_long_range_B_other8.087
r_dihedral_angle_1_deg6.073
r_scangle_other4.398
r_scbond_it2.903
r_scbond_other2.894
r_mcangle_it2.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.629
r_dihedral_angle_4_deg15.913
r_dihedral_angle_3_deg13.18
r_long_range_B_refined8.129
r_long_range_B_other8.087
r_dihedral_angle_1_deg6.073
r_scangle_other4.398
r_scbond_it2.903
r_scbond_other2.894
r_mcangle_it2.62
r_mcangle_other2.617
r_mcbond_it1.877
r_mcbond_other1.865
r_angle_refined_deg1.781
r_angle_other_deg1.043
r_chiral_restr0.109
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms4069
Nucleic Acid Atoms
Solvent Atoms581
Heterogen Atoms136

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing