8AHU

Crystal structure of D-amino acid aminotrensferase from Haliscomenobacter hydrossis complexed with D-cycloserine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7P7X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2880.1M sodium acetate pH 4.8, 16-22% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.5251.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.902α = 90
b = 71.94β = 101.47
c = 53.089γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.9SPring-8BL41XU

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
11.4142.5899.70.0790.0860.0340.9986.56.461465
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)
11.411.4399.90.4330.4730.1880.9466

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 REPLACEMENTTHROUGHOUT7P7X1.4142.5858305300299.460.17320.17170.2028RANDOM21.939
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]
0.2-2.12-0.541.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.005
r_dihedral_angle_4_deg21.059
r_dihedral_angle_3_deg13.696
r_dihedral_angle_1_deg7.015
r_angle_refined_deg2.006
r_angle_other_deg1.529
r_chiral_restr0.11
r_bond_refined_d0.016
r_gen_planes_refined0.014
r_gen_planes_other0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.005
r_dihedral_angle_4_deg21.059
r_dihedral_angle_3_deg13.696
r_dihedral_angle_1_deg7.015
r_angle_refined_deg2.006
r_angle_other_deg1.529
r_chiral_restr0.11
r_bond_refined_d0.016
r_gen_planes_refined0.014
r_gen_planes_other0.004
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2269
Nucleic Acid Atoms
Solvent Atoms267
Heterogen Atoms35

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
REFMACphasing