8VR3

crystal structure of the Pcryo_0618 aminotransferase from Psychrobacter cryohalolentis K5 in the presence of its internal aldimine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BN1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5293Protein incubated with 5 mM UDP and 5 mM PLP. Precipitant: 18-22% PEG 5000, 200 mM tetraethylammonium chloride, and 100 mM Homo-PIPES (pH 5)
Crystal Properties
Matthews coefficientSolvent content
3.6165.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.019α = 90
b = 157.97β = 90
c = 130.591γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON II2019-04-16MSINGLE 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
125099.20.09112.510.280593
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)
122.197.30.462.45.1

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 REPLACEMENTTHROUGHOUT232.6576621397299.240.199270.197530.23276RANDOM22.965
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.327
r_dihedral_angle_2_deg13.258
r_long_range_B_refined7.019
r_long_range_B_other7.019
r_dihedral_angle_1_deg6.61
r_scangle_other5.24
r_scbond_it3.234
r_scbond_other3.234
r_mcangle_it3.209
r_mcangle_other3.209
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.327
r_dihedral_angle_2_deg13.258
r_long_range_B_refined7.019
r_long_range_B_other7.019
r_dihedral_angle_1_deg6.61
r_scangle_other5.24
r_scbond_it3.234
r_scbond_other3.234
r_mcangle_it3.209
r_mcangle_other3.209
r_mcbond_it2.087
r_mcbond_other2.084
r_angle_refined_deg1.609
r_angle_other_deg0.5
r_chiral_restr0.068
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.002
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 Atoms5784
Nucleic Acid Atoms
Solvent Atoms517
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing