5Y8M

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


X-RAY DIFFRACTION

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
2.8656.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.02α = 90
b = 129.02β = 90
c = 70.3γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2015-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
12.04111.7399.10.1811.29.542572
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)
12.042.1599.10.1811.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.04111.7340373214199.80.1540.1520.198RANDOM21.34
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]
-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.877
r_dihedral_angle_4_deg18.65
r_dihedral_angle_3_deg13.384
r_dihedral_angle_1_deg7.155
r_long_range_B_other6.514
r_long_range_B_refined6.513
r_scangle_other4.171
r_scbond_it2.858
r_scbond_other2.854
r_mcangle_it2.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.877
r_dihedral_angle_4_deg18.65
r_dihedral_angle_3_deg13.384
r_dihedral_angle_1_deg7.155
r_long_range_B_other6.514
r_long_range_B_refined6.513
r_scangle_other4.171
r_scbond_it2.858
r_scbond_other2.854
r_mcangle_it2.094
r_mcangle_other2.094
r_angle_refined_deg1.947
r_mcbond_it1.537
r_mcbond_other1.503
r_angle_other_deg1.093
r_chiral_restr0.122
r_bond_refined_d0.018
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 Atoms4039
Nucleic Acid Atoms
Solvent Atoms551
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing