5I5U

X-RAY CRYSTAL STRUCTURE AT 2.40A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A TETRAHYDRONAPHTHALENYL 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
2.3647.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.074α = 90
b = 105.995β = 90
c = 107.462γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A200VARIMAX HF2010-09-04MSINGLE 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
12.404107.46299.90.08814.85.23139842.5
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)
12.4042.531000.5021.65.2

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 structure2.4042029753157999.80.17050.16710.2335RANDOM35.289
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]
-2.010.941.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.667
r_dihedral_angle_4_deg13.338
r_dihedral_angle_3_deg12.816
r_mcangle_it4.547
r_dihedral_angle_1_deg4.308
r_mcbond_it2.9
r_mcbond_other2.895
r_angle_refined_deg1.463
r_angle_other_deg0.748
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.667
r_dihedral_angle_4_deg13.338
r_dihedral_angle_3_deg12.816
r_mcangle_it4.547
r_dihedral_angle_1_deg4.308
r_mcbond_it2.9
r_mcbond_other2.895
r_angle_refined_deg1.463
r_angle_other_deg0.748
r_chiral_restr0.077
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5775
Nucleic Acid Atoms
Solvent Atoms518
Heterogen Atoms96

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing