1EKV

HUMAN BRANCHED CHAIN AMINO ACID AMINOTRANSFERASE (MITOCHONDRIAL): THREE DIMENSIONAL STRUCTURE OF ENZYME INACTIVATED BY TRIS BOUND TO THE PYRIDOXAL-5'-PHOSPHATE ON ONE END AND ACTIVE SITE LYS202 NZ ON THE OTHER.


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.2
Temperature 298.0
Details AMMONIUM SULPHATE, DTT, TRIS, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 83.74 α = 90
b = 83.74 β = 90
c = 104.81 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 223
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 1998-03-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.25 34.27 82.8 0.127 -- -- 1.8 32336 32336 0.0 0.0 10.8
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.25 2.33 69.4 0.263 -- -- 2.29 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
-- 2.25 34.27 0.0 2.0 31372 24049 2389 63.3 0.231 0.195 0.189 0.25 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.27 2.41 -- 285 2377 0.199 0.278 0.016 42.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 20.2
Anisotropic B[1][1] -1.43
Anisotropic B[1][2] 1.63
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.43
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.87
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.012
c_angle_deg 1.7
c_improper_angle_d 1.13
c_dihedral_angle_d 24.2
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Sigma A (Observed) 0.19
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.33
Luzzati Sigma A (R-Free Set) 0.29
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5820
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 212

Software

Software
Software Name Purpose
AMoRE phasing
CNS refinement version: 0.9
DENZO data reduction
SCALEPACK data scaling