5I5Y

X-RAY CRYSTAL STRUCTURE AT 1.81A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH AN ARYL ACETATE 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
2.3146.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.92α = 90
b = 109.92β = 96.98
c = 59.918γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A200VARIMAX HF2011-05-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
11.814098.60.06910.93.56788021.6
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)
11.811.8497.50.213.4

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 structure1.812065110273398.480.15170.15010.1897RANDOM23.855
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]
-0.4-0.310.060.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.88
r_dihedral_angle_4_deg12.521
r_dihedral_angle_3_deg10.389
r_dihedral_angle_1_deg4.482
r_mcangle_it2.587
r_mcbond_it1.61
r_mcbond_other1.609
r_angle_refined_deg1.373
r_angle_other_deg0.728
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.88
r_dihedral_angle_4_deg12.521
r_dihedral_angle_3_deg10.389
r_dihedral_angle_1_deg4.482
r_mcangle_it2.587
r_mcbond_it1.61
r_mcbond_other1.609
r_angle_refined_deg1.373
r_angle_other_deg0.728
r_chiral_restr0.076
r_bond_refined_d0.007
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 Atoms5766
Nucleic Acid Atoms
Solvent Atoms1048
Heterogen Atoms124

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
REFMACphasing