8AYJ

Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiens complexed with 3-aminooxypropionic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2880.02 M Sodium/potassium phosphate,0.1 M Bis-Tris propane pH 6.5, 20 % w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.346.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.573α = 90
b = 58.434β = 94.11
c = 96.722γ = 90
Symmetry
Space GroupP 1 21 1

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
11.7548.2498.90.1620.1960.1090.994.3356226
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)
11.751.7895.41.1241.3630.7610.4252.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT8AHR1.7548.2453435277498.870.20290.2010.2393RANDOM14.988
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]
0.950.24-0.96-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.558
r_dihedral_angle_4_deg17.995
r_dihedral_angle_3_deg13.491
r_dihedral_angle_1_deg7.386
r_angle_refined_deg1.878
r_angle_other_deg1.409
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.558
r_dihedral_angle_4_deg17.995
r_dihedral_angle_3_deg13.491
r_dihedral_angle_1_deg7.386
r_angle_refined_deg1.878
r_angle_other_deg1.409
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4285
Nucleic Acid Atoms
Solvent Atoms406
Heterogen Atoms122

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing