2Z9U

Crystal structure of pyridoxamine-pyruvate aminotransferase from Mesorhizobium loti at 2.0 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VJOPDB ID 1VJO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.052770.1M HEPES, 2M Ammonium sulfate, pH 8.05, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.244.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.545α = 90
b = 68.545β = 90
c = 311.635γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS V2006-04-10MSINGLE 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
11.95097.80.08410.6558804-318.89
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)
11.91.9797.20.3795.65701

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 1VJO21547892255197.930.158090.155580.20553RANDOM18.596
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_it3.224
r_scbond_it2.106
r_angle_refined_deg1.44
r_mcangle_it1.119
r_mcbond_it0.729
r_nbtor_refined0.306
r_symmetry_hbond_refined0.203
r_nbd_refined0.198
r_symmetry_vdw_refined0.174
r_xyhbond_nbd_refined0.139
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it3.224
r_scbond_it2.106
r_angle_refined_deg1.44
r_mcangle_it1.119
r_mcbond_it0.729
r_nbtor_refined0.306
r_symmetry_hbond_refined0.203
r_nbd_refined0.198
r_symmetry_vdw_refined0.174
r_xyhbond_nbd_refined0.139
r_chiral_restr0.099
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5832
Nucleic Acid Atoms
Solvent Atoms550
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection