2ZYJ

Crystal structure of LysN, alpha-aminoadipate aminotransferase (complexed with N-(5'-phosphopyridoxyl)-L-glutamate), from Thermus thermophilus HB27


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CBF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729316% PEG 3350, 0.1M HEPES, 0.2M Calcium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2444.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.761α = 90
b = 93.346β = 90
c = 150.827γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 210mirrors2009-01-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A0.978Photon FactoryBL-6A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.675099.20.0970.097919222.22.2
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)
11.671.7399.80.5889045

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3CBF1.6730.4786525456398.960.196040.193370.24611RANDOM16.178
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.488
r_dihedral_angle_4_deg19.936
r_dihedral_angle_3_deg15.844
r_dihedral_angle_1_deg5.568
r_scangle_it3.3
r_scbond_it2.091
r_angle_refined_deg1.515
r_mcangle_it1.245
r_mcbond_it0.81
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.488
r_dihedral_angle_4_deg19.936
r_dihedral_angle_3_deg15.844
r_dihedral_angle_1_deg5.568
r_scangle_it3.3
r_scbond_it2.091
r_angle_refined_deg1.515
r_mcangle_it1.245
r_mcbond_it0.81
r_nbtor_refined0.307
r_symmetry_hbond_refined0.225
r_nbd_refined0.206
r_symmetry_vdw_refined0.184
r_xyhbond_nbd_refined0.182
r_chiral_restr0.099
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6188
Nucleic Acid Atoms
Solvent Atoms956
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing