5Y8O

Mycobacterium tuberculosis 3-Hydroxyisobutyrate dehydrogenase (MtHIBADH) + NAD + 3-Hydroxy propionate (3-HP)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OBB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH2950.02M MgCl2.6H2O, 0.1M HEPES pH 7.5, 22% w/v polyacrylic acid sodium salt 5100
Crystal Properties
Matthews coefficientSolvent content
2.8356.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.06α = 90
b = 129.06β = 90
c = 70.13γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2017-08-10MSINGLE 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
12.05111.77990.1663.641484
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)
12.052.16990.166

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 REPLACEMENTTHROUGHOUT3OBB2.05111.7739313209598.890.178190.17570.22508RANDOM23.308
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]
0.110.050.11-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.452
r_dihedral_angle_4_deg20.566
r_dihedral_angle_3_deg14.957
r_long_range_B_refined7.596
r_long_range_B_other7.539
r_dihedral_angle_1_deg6.1
r_scangle_other3.917
r_scbond_it2.501
r_scbond_other2.499
r_mcangle_other2.331
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.452
r_dihedral_angle_4_deg20.566
r_dihedral_angle_3_deg14.957
r_long_range_B_refined7.596
r_long_range_B_other7.539
r_dihedral_angle_1_deg6.1
r_scangle_other3.917
r_scbond_it2.501
r_scbond_other2.499
r_mcangle_other2.331
r_mcangle_it2.33
r_angle_refined_deg1.619
r_mcbond_it1.517
r_mcbond_other1.479
r_angle_other_deg1.019
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.008
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 Atoms4097
Nucleic Acid Atoms
Solvent Atoms518
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing