5F8V

Crystal structure of PLP bound phosphoserine aminotransferase (PSAT) from Trichomonas vaginalis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP28925-30% PEG 3350 (w/v),100mM sodium acetate pH 4.5-5.0, 200mM sodium malonate, 10% glycerol (v/v)
Crystal Properties
Matthews coefficientSolvent content
2.4549.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.967α = 90
b = 235.434β = 90.02
c = 134.52γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2014-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.145099.90.157.93.717742932.43
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)
12.142.2399.80.443.33.6

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 REPLACEMENTTHROUGHOUT1BJN2.1437.42168230904199.40.210220.208690.23905RANDOM24.791
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]
0.116.77-4.374.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.318
r_dihedral_angle_4_deg15.758
r_dihedral_angle_3_deg13.726
r_dihedral_angle_1_deg6.763
r_long_range_B_refined2.562
r_long_range_B_other2.555
r_mcangle_it1.381
r_mcangle_other1.381
r_scangle_other1.318
r_angle_refined_deg1.253
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.318
r_dihedral_angle_4_deg15.758
r_dihedral_angle_3_deg13.726
r_dihedral_angle_1_deg6.763
r_long_range_B_refined2.562
r_long_range_B_other2.555
r_mcangle_it1.381
r_mcangle_other1.381
r_scangle_other1.318
r_angle_refined_deg1.253
r_angle_other_deg0.912
r_mcbond_it0.813
r_mcbond_other0.813
r_scbond_it0.769
r_scbond_other0.769
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms22852
Nucleic Acid Atoms
Solvent Atoms749
Heterogen Atoms

Software

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