2PB2

Structure of biosynthetic N-acetylornithine aminotransferase from Salmonella typhimurium: studies on substrate specificity and inhibitor binding


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OAThuman Ornithine aminotransferase

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729820% PEG3350, 0.5M Ammonium acetate, 0.1M HEPES, 1mM Gabaculine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0339.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.065α = 90
b = 111.966β = 90
c = 65.489γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOsmic Mirrors2006-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.93091.80.0711913.5558715129023.2
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)
11.91.9780.70.3933.45525

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 REPLACEMENTTHROUGHOUThuman Ornithine aminotransferase1.9129.5948704257791.840.197740.195740.23653RANDOM20.319
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.551
r_dihedral_angle_4_deg13.91
r_dihedral_angle_3_deg13.337
r_dihedral_angle_1_deg5.03
r_scangle_it1.09
r_angle_refined_deg0.93
r_scbond_it0.668
r_mcangle_it0.439
r_nbtor_refined0.299
r_mcbond_it0.258
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.551
r_dihedral_angle_4_deg13.91
r_dihedral_angle_3_deg13.337
r_dihedral_angle_1_deg5.03
r_scangle_it1.09
r_angle_refined_deg0.93
r_scbond_it0.668
r_mcangle_it0.439
r_nbtor_refined0.299
r_mcbond_it0.258
r_nbd_refined0.17
r_symmetry_vdw_refined0.143
r_xyhbond_nbd_refined0.086
r_symmetry_hbond_refined0.073
r_chiral_restr0.064
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5744
Nucleic Acid Atoms
Solvent Atoms573
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing