5Y8K

Mycobacterium tuberculosis 3-Hydroxyisobutyrate dehydrogenase (MtHIBADH) + L-serine


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
2.8656.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.4α = 90
b = 129.4β = 90
c = 70.57γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2015-10-12MSINGLE 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
12.04112.0696.40.176710.142645
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)
12.042.1596.40.1767

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 REPLACEMENTTHROUGHOUT3OBB2.04112.06404222153990.1690.1670.206RANDOM24.47
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]
0.120.060.12-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.302
r_dihedral_angle_4_deg16.761
r_dihedral_angle_3_deg13.425
r_long_range_B_refined6.703
r_long_range_B_other6.018
r_dihedral_angle_1_deg5.782
r_scangle_other2.517
r_mcangle_it1.64
r_mcangle_other1.63
r_scbond_it1.556
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.302
r_dihedral_angle_4_deg16.761
r_dihedral_angle_3_deg13.425
r_long_range_B_refined6.703
r_long_range_B_other6.018
r_dihedral_angle_1_deg5.782
r_scangle_other2.517
r_mcangle_it1.64
r_mcangle_other1.63
r_scbond_it1.556
r_scbond_other1.556
r_angle_refined_deg1.353
r_mcbond_it1.008
r_mcbond_other0.994
r_angle_other_deg0.954
r_chiral_restr0.079
r_bond_refined_d0.008
r_gen_planes_refined0.006
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 Atoms4074
Nucleic Acid Atoms
Solvent Atoms716
Heterogen Atoms73

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing