3CBF

Crystal structure of LysN, alpha-aminoadipate aminotransferase, from Thermus thermophilus HB27


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Z1YPDB ENTRY 2Z1Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.329318% PEG3350, 0.2M potassium fluoride, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2144.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.279α = 90
b = 93.243β = 90
c = 150.88γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4mirrors2008-02-09MSINGLE 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
11.67501000.0660.06630.16.6912339123322
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.671.731000.5560.5566.68322

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2Z1Y1.6734.698372583725441596.770.204150.204150.201910.24709RANDOM23.772
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.507
r_dihedral_angle_4_deg19.835
r_dihedral_angle_3_deg16.109
r_dihedral_angle_1_deg5.641
r_scangle_it3.529
r_scbond_it2.212
r_angle_refined_deg1.491
r_mcangle_it1.359
r_mcbond_it0.854
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.507
r_dihedral_angle_4_deg19.835
r_dihedral_angle_3_deg16.109
r_dihedral_angle_1_deg5.641
r_scangle_it3.529
r_scbond_it2.212
r_angle_refined_deg1.491
r_mcangle_it1.359
r_mcbond_it0.854
r_nbtor_refined0.308
r_symmetry_vdw_refined0.246
r_nbd_refined0.205
r_xyhbond_nbd_refined0.172
r_symmetry_hbond_refined0.158
r_chiral_restr0.098
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6156
Nucleic Acid Atoms
Solvent Atoms431
Heterogen Atoms52

Software

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