8VR5

crystal structure of the Pcryo_0618 aminotransferase from Psychrobacter cryohalolentis K5 in the presence of PMP and glutamate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8VR3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5293Protein incubated with 1.0 mM PLP and 5 mM UDP-4-amino-2,3-diacetoamido-2,3,4-trideoxy-L-arabinose. Precipitant: 8-12% PEG 8000, 100 mM magnesium chloride, and 100 mM Homo-PIPES (pH 5)
Crystal Properties
Matthews coefficientSolvent content
3.6165.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.493α = 90
b = 159.822β = 90
c = 115.864γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON II2019-08-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEBRUKER D8 QUEST1.5418

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
12.25099.60.07815.68.3123706
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.398.90.343.25.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.232.89117412629799.650.179980.178160.21348RANDOM22.968
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.119
r_dihedral_angle_2_deg8.745
r_long_range_B_refined7.247
r_long_range_B_other7.247
r_dihedral_angle_1_deg6.723
r_scangle_other5.689
r_mcangle_it3.665
r_mcangle_other3.665
r_scbond_it3.461
r_scbond_other3.461
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.119
r_dihedral_angle_2_deg8.745
r_long_range_B_refined7.247
r_long_range_B_other7.247
r_dihedral_angle_1_deg6.723
r_scangle_other5.689
r_mcangle_it3.665
r_mcangle_other3.665
r_scbond_it3.461
r_scbond_other3.461
r_mcbond_it2.311
r_mcbond_other2.31
r_angle_refined_deg1.572
r_angle_other_deg0.508
r_chiral_restr0.116
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms11583
Nucleic Acid Atoms
Solvent Atoms857
Heterogen Atoms185

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing