3HT5 | pdb_00003ht5

Crystal Structure of IlvE a Branched Chain Amino Acid Transaminase from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HHF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.82980.05 M HEPES HCL pH 7.0, 1% Trytpone, 12% PEG 3350, under oil, sitting drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.141.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.454α = 90
b = 85.351β = 90
c = 59.715γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4DOUBLY FOCUSING TOROIDAL MIRROR2008-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12BNSLSX12B

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
11.939.299.60.0727.74.92689722.9
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)
1.921000.3861.94.9

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2HHF1.939.1926897135199.30.1850.1840.190.1980.2RANDOM23.48
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.995
r_dihedral_angle_3_deg13.657
r_dihedral_angle_4_deg13.623
r_dihedral_angle_1_deg5.775
r_scangle_it2.442
r_scbond_it1.467
r_angle_refined_deg1.367
r_mcangle_it0.979
r_mcbond_it0.517
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.995
r_dihedral_angle_3_deg13.657
r_dihedral_angle_4_deg13.623
r_dihedral_angle_1_deg5.775
r_scangle_it2.442
r_scbond_it1.467
r_angle_refined_deg1.367
r_mcangle_it0.979
r_mcbond_it0.517
r_nbtor_refined0.305
r_nbd_refined0.193
r_symmetry_vdw_refined0.151
r_symmetry_hbond_refined0.147
r_chiral_restr0.129
r_xyhbond_nbd_refined0.12
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_refined
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2567
Nucleic Acid Atoms
Solvent Atoms281
Heterogen Atoms16

Software

Software
Software NamePurpose
MOSFLMdata reduction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
PHENIXphasing