9J0V

Crystal structure of monomeric PLP-dependent transaminase from Desulfobacula toluolica in P 21 21 21 space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2880.1M Ammonium acetate, 0.1M Bis-tris pH 5.5, 17% PEG 10000
Crystal Properties
Matthews coefficientSolvent content
1.9737.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.847α = 90
b = 56.226β = 90
c = 118.625γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.88560ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.7940.8198.80.0470.0560.0280.99813.43.624352
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.791.8396.20.670.7870.4050.6863.4

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 REPLACEMENTTHROUGHOUT1.7940.8123150114698.510.195220.193250.23575RANDOM38.029
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]
-0.15-0.80.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.653
r_dihedral_angle_4_deg18.155
r_dihedral_angle_3_deg15.413
r_long_range_B_other9.677
r_long_range_B_refined9.664
r_scangle_other7.953
r_dihedral_angle_1_deg7.366
r_mcangle_it6.148
r_mcangle_other6.146
r_scbond_it5.892
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.653
r_dihedral_angle_4_deg18.155
r_dihedral_angle_3_deg15.413
r_long_range_B_other9.677
r_long_range_B_refined9.664
r_scangle_other7.953
r_dihedral_angle_1_deg7.366
r_mcangle_it6.148
r_mcangle_other6.146
r_scbond_it5.892
r_scbond_other5.889
r_mcbond_other4.779
r_mcbond_it4.776
r_angle_refined_deg2.1
r_angle_other_deg1.501
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.013
r_gen_planes_other0.004
r_bond_other_d0.003
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 Atoms1872
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction