5Y8G

Mycobacterium tuberculosis 3-Hydroxyisobutyrate Dehydrogenase (MtHIBADH)


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
2.7956

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.79α = 90
b = 128.79β = 90
c = 70.35γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2015-09-22MSINGLE 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
12.01111.541002.78.244342
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)
12.012.121000.144

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 REPLACEMENTTHROUGHOUT3OBB2.01111.5442055223499.90.1460.1440.185RANDOM21.18
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]
-0.03-0.02-0.030.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.179
r_dihedral_angle_4_deg22.008
r_dihedral_angle_3_deg13.495
r_long_range_B_refined7.142
r_long_range_B_other6.953
r_dihedral_angle_1_deg6.088
r_scangle_other4.646
r_scbond_it3.072
r_scbond_other3.071
r_mcangle_it2.331
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.179
r_dihedral_angle_4_deg22.008
r_dihedral_angle_3_deg13.495
r_long_range_B_refined7.142
r_long_range_B_other6.953
r_dihedral_angle_1_deg6.088
r_scangle_other4.646
r_scbond_it3.072
r_scbond_other3.071
r_mcangle_it2.331
r_mcangle_other2.327
r_angle_refined_deg1.845
r_mcbond_it1.639
r_mcbond_other1.631
r_angle_other_deg1.103
r_chiral_restr0.119
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 Atoms4083
Nucleic Acid Atoms
Solvent Atoms710
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing