2Z9V

Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxamine


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 Pyridoxamine, pH 8.05, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2144.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.628α = 90
b = 68.628β = 90
c = 312.191γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS V2005-10-27MSINGLE 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
11.75098.40.03924.45.882435-314.99
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)
11.71.7691.90.11337561

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 2Z9U1.714.9478010409498.440.157140.155590.18636RANDOM14.852
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_it2.772
r_scbond_it1.758
r_angle_refined_deg1.248
r_mcangle_it0.89
r_mcbond_it0.56
r_symmetry_hbond_refined0.43
r_nbtor_refined0.308
r_nbd_refined0.198
r_symmetry_vdw_refined0.155
r_xyhbond_nbd_refined0.116
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it2.772
r_scbond_it1.758
r_angle_refined_deg1.248
r_mcangle_it0.89
r_mcbond_it0.56
r_symmetry_hbond_refined0.43
r_nbtor_refined0.308
r_nbd_refined0.198
r_symmetry_vdw_refined0.155
r_xyhbond_nbd_refined0.116
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 Atoms753
Heterogen Atoms73

Software

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