8YRT

Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis in the holo form obtained at pH 7.0


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP728845% v/v Tacsimate pH 7.0, 0.1 M BIS-TRIS propane pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.4549.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.043α = 90
b = 71.902β = 100.14
c = 52.015γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HE2023-05-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54

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
1221.9699.70.0750.0810.0320.99823.76.621090
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)
122.0597.60.3910.4250.1640.9266.6

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 REPLACEMENTTHROUGHOUT221.962010098899.710.147160.145050.19038RANDOM23.137
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]
0.33-0.82-0.170.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.848
r_dihedral_angle_2_deg10.611
r_long_range_B_other8.1
r_long_range_B_refined8.096
r_dihedral_angle_1_deg6.993
r_scangle_other6.583
r_scbond_other4.412
r_scbond_it4.407
r_mcangle_it3.632
r_mcangle_other3.632
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.848
r_dihedral_angle_2_deg10.611
r_long_range_B_other8.1
r_long_range_B_refined8.096
r_dihedral_angle_1_deg6.993
r_scangle_other6.583
r_scbond_other4.412
r_scbond_it4.407
r_mcangle_it3.632
r_mcangle_other3.632
r_mcbond_it2.767
r_mcbond_other2.762
r_angle_refined_deg2.285
r_angle_other_deg0.759
r_chiral_restr0.108
r_bond_refined_d0.015
r_gen_planes_refined0.013
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 Atoms2273
Nucleic Acid Atoms
Solvent Atoms116
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
CrysalisProdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction