8ONL

Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense point mutant E113A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52880.2 M NaNitrate, 0.1 M Bis-tris propane pH 6.5, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1843.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.429α = 90
b = 88.013β = 90
c = 99.772γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2022-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONKURCHATOV SNC BEAMLINE K4.40.74503KURCHATOV SNCK4.4

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
11.944.9799.70.110.1220.0520.99710.45.443170
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)
11.91.941000.690.7630.3210.7315.5

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 REPLACEMENTTHROUGHOUT1.933.740996215699.510.215770.213280.26317RANDOM26.428
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]
-1.521.79-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.173
r_dihedral_angle_4_deg17.082
r_dihedral_angle_3_deg15.252
r_dihedral_angle_1_deg7.526
r_long_range_B_refined5.93
r_long_range_B_other5.874
r_scangle_other4.531
r_mcangle_it3.715
r_mcangle_other3.715
r_scbond_it3.135
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.173
r_dihedral_angle_4_deg17.082
r_dihedral_angle_3_deg15.252
r_dihedral_angle_1_deg7.526
r_long_range_B_refined5.93
r_long_range_B_other5.874
r_scangle_other4.531
r_mcangle_it3.715
r_mcangle_other3.715
r_scbond_it3.135
r_scbond_other3.135
r_mcbond_it2.615
r_mcbond_other2.615
r_angle_refined_deg1.798
r_angle_other_deg1.312
r_chiral_restr0.091
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.002
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 Atoms4207
Nucleic Acid Atoms
Solvent Atoms267
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
REFMACphasing
PDB_EXTRACTdata extraction