5I5T

X-RAY CRYSTAL STRUCTURE AT 2.31A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A TETRAHYDROQUINOLINE 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
2.3748

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.03α = 90
b = 106.1β = 90
c = 107.798γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A200VARIMAX HF2010-09-03MSINGLE 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
12.308107.79899.50.09314.85.43530636.4
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)
12.312.4399.80.4971.55.4

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 structure2.312033427175099.220.17050.16720.2346RANDOM33.525
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]
-2.261.320.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.925
r_dihedral_angle_4_deg12.711
r_dihedral_angle_3_deg12.089
r_dihedral_angle_1_deg4.347
r_mcangle_it4.119
r_mcbond_it2.628
r_mcbond_other2.627
r_angle_refined_deg1.427
r_angle_other_deg0.751
r_chiral_restr0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.925
r_dihedral_angle_4_deg12.711
r_dihedral_angle_3_deg12.089
r_dihedral_angle_1_deg4.347
r_mcangle_it4.119
r_mcbond_it2.628
r_mcbond_other2.627
r_angle_refined_deg1.427
r_angle_other_deg0.751
r_chiral_restr0.079
r_bond_refined_d0.009
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 Atoms5726
Nucleic Acid Atoms
Solvent Atoms625
Heterogen Atoms96

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing