2Z9X

Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxyl-L-alanine


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, 5mM Pyridoxyl-L-alanine, pH 8.05, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2244.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.72α = 90
b = 68.72β = 90
c = 311.942γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS V2006-12-13MSINGLE 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
11.945098.60.07156030-3
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)
11.942.01970.279.75397

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 2Z9U1.9414.9252891282798.520.146570.144570.1837RANDOM18.258
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_it3.06
r_scbond_it1.982
r_angle_refined_deg1.342
r_mcangle_it1.039
r_mcbond_it0.687
r_nbtor_refined0.304
r_nbd_refined0.197
r_symmetry_vdw_refined0.18
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.143
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it3.06
r_scbond_it1.982
r_angle_refined_deg1.342
r_mcangle_it1.039
r_mcbond_it0.687
r_nbtor_refined0.304
r_nbd_refined0.197
r_symmetry_vdw_refined0.18
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.143
r_chiral_restr0.093
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_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 Atoms5832
Nucleic Acid Atoms
Solvent Atoms614
Heterogen Atoms136

Software

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