5Y8L

Mycobacterium tuberculosis 3-Hydroxyisobutyrate dehydrogenase (MtHIBADH) + NAD +(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
2.8456.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.79α = 90
b = 128.79β = 90
c = 70.22γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEBruker PHOTON II2015-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER D8 QUEST0.95372

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
11.85111.541000.1617.65.356709
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)
11.851.951000.1617.6

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 REPLACEMENTTHROUGHOUT3OBB1.85111.545381228751000.1440.1420.183RANDOM20.12
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]
0.250.120.25-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.691
r_dihedral_angle_4_deg16.339
r_dihedral_angle_3_deg13.096
r_long_range_B_refined7.227
r_long_range_B_other7.227
r_dihedral_angle_1_deg6.149
r_scangle_other4.456
r_scbond_it2.975
r_scbond_other2.972
r_mcangle_it2.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.691
r_dihedral_angle_4_deg16.339
r_dihedral_angle_3_deg13.096
r_long_range_B_refined7.227
r_long_range_B_other7.227
r_dihedral_angle_1_deg6.149
r_scangle_other4.456
r_scbond_it2.975
r_scbond_other2.972
r_mcangle_it2.1
r_mcangle_other2.1
r_angle_refined_deg1.94
r_mcbond_it1.485
r_mcbond_other1.485
r_angle_other_deg1.115
r_chiral_restr0.123
r_bond_refined_d0.019
r_gen_planes_refined0.01
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 Atoms4101
Nucleic Acid Atoms
Solvent Atoms748
Heterogen Atoms149

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing