8X1F

Crystal structure of an omega-transaminase mutant from Aspergillus terreus with in complex with PLP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CE5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6291.15100 mM citrate buffer (pH 5.6) 200 mM ammonium acetate 30% (w/v) PEG-MME 4000 0.1 mM pyridoxal phosphate
Crystal Properties
Matthews coefficientSolvent content
3.8167.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.436α = 90
b = 113.983β = 91.56
c = 101.424γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2023-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.9785SSRFBL18U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.34797.60.1260.1620.16.13.94647134.89
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3898.40.5560.7160.4463.9

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 REPLACEMENTTHROUGHOUT2.34743949251997.460.223330.22110.26246RANDOM36.916
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]
1.45-5.73-2.611.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.035
r_dihedral_angle_2_deg8.599
r_dihedral_angle_1_deg7.272
r_long_range_B_refined5.863
r_long_range_B_other5.855
r_scangle_other4.405
r_mcangle_it3.899
r_mcangle_other3.899
r_scbond_it2.907
r_scbond_other2.906
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.035
r_dihedral_angle_2_deg8.599
r_dihedral_angle_1_deg7.272
r_long_range_B_refined5.863
r_long_range_B_other5.855
r_scangle_other4.405
r_mcangle_it3.899
r_mcangle_other3.899
r_scbond_it2.907
r_scbond_other2.906
r_mcbond_it2.63
r_mcbond_other2.625
r_angle_refined_deg1.452
r_angle_other_deg0.492
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.006
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 Atoms5028
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
HKL-3000data reduction
AMPLEphasing
PDB_EXTRACTdata extraction