2Z9W

Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxal


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Z9UPDB ID 2Z9U

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.052770.1M HEPES, 2M Ammonium sulfate, 10mM Pyridoxal, pH 8.05, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2244.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.732α = 90
b = 68.732β = 90
c = 311.5γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS V2005-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.0000SPring-8BL38B1

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
11.65099.90.0849.97.4100019-313.27
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)
11.61.6699.90.3867.49737

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 REPLACEMENTTHROUGHOUTPDB ID 2Z9U1.714.8479313412399.970.155430.154110.18051RANDOM12.8
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_scangle_it2.789
r_scbond_it1.809
r_angle_refined_deg1.243
r_mcangle_it0.926
r_mcbond_it0.573
r_nbtor_refined0.308
r_nbd_refined0.2
r_symmetry_vdw_refined0.178
r_symmetry_hbond_refined0.178
r_xyhbond_nbd_refined0.126
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it2.789
r_scbond_it1.809
r_angle_refined_deg1.243
r_mcangle_it0.926
r_mcbond_it0.573
r_nbtor_refined0.308
r_nbd_refined0.2
r_symmetry_vdw_refined0.178
r_symmetry_hbond_refined0.178
r_xyhbond_nbd_refined0.126
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5832
Nucleic Acid Atoms
Solvent Atoms778
Heterogen Atoms99

Software

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