5I5V

X-RAY CRYSTAL STRUCTURE AT 1.94A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A THIENOPYRIMIDINE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIn-house structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293MDL MORPHEUS SCREEN CONDITION B2, DTT
Crystal Properties
Matthews coefficientSolvent content
2.3547.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.5α = 90
b = 105.537β = 90
c = 106.829γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONOTHER0.9763

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
11.944099.70.0999.25.458670
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)
11.941.9799.30.5065.3

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTIn-house structure1.942056229236999.530.17140.16910.2264RANDOM31.007
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]
-1.650.251.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.21
r_dihedral_angle_4_deg12.721
r_dihedral_angle_3_deg11.382
r_dihedral_angle_1_deg4.298
r_mcangle_it3.368
r_mcbond_it2.173
r_mcbond_other2.171
r_angle_refined_deg1.325
r_angle_other_deg0.72
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.21
r_dihedral_angle_4_deg12.721
r_dihedral_angle_3_deg11.382
r_dihedral_angle_1_deg4.298
r_mcangle_it3.368
r_mcbond_it2.173
r_mcbond_other2.171
r_angle_refined_deg1.325
r_angle_other_deg0.72
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5750
Nucleic Acid Atoms
Solvent Atoms750
Heterogen Atoms138

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
REFMACphasing