2VHW

Crystal structure of holo L-alanine dehydrogenase from Mycobacterium tuberculosis in the open and closed conformation


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
113% ETHANOL, 0.2M MGCL2 AND 0.1 M HEPES PH7.4
Crystal Properties
Matthews coefficientSolvent content
2.9557.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.028α = 90
b = 172.015β = 90
c = 98.556γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
1249.61000.110.142011262.3
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)
122.111000.62.33.9

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 REPLACEMENTTHROUGHOUT2401914241015099.40.1780.1760.212RANDOM44.75
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]
-1.04-0.361.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.166
r_dihedral_angle_4_deg18.218
r_dihedral_angle_3_deg15.519
r_dihedral_angle_1_deg6.031
r_scangle_it2.915
r_scbond_it1.87
r_angle_refined_deg1.504
r_mcangle_it1.064
r_mcbond_it0.662
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.166
r_dihedral_angle_4_deg18.218
r_dihedral_angle_3_deg15.519
r_dihedral_angle_1_deg6.031
r_scangle_it2.915
r_scbond_it1.87
r_angle_refined_deg1.504
r_mcangle_it1.064
r_mcbond_it0.662
r_nbtor_refined0.299
r_symmetry_hbond_refined0.237
r_nbd_refined0.197
r_symmetry_vdw_refined0.168
r_xyhbond_nbd_refined0.139
r_chiral_restr0.099
r_metal_ion_refined0.015
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16344
Nucleic Acid Atoms
Solvent Atoms1512
Heterogen Atoms266

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing