7P8O

Crystal structure of D-aminoacid transaminase from Haliscomenobacter hydrossis in its intermediate form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CM0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP288MES 0.1 M pH 6.5; MgSO4; 1.8 M NaCl.
Crystal Properties
Matthews coefficientSolvent content
2.550.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.636α = 90
b = 72.374β = 100.05
c = 51.822γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.97ESRFMASSIF-3

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
11.9551.0397.50.0480.0590.0330.99810.92.922696
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)
11.95295.60.3940.4760.2650.8853

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 REPLACEMENTTHROUGHOUT5CM01.9539.8721576110597.350.193230.191150.23153RANDOM32.572
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]
0.53-2.25-0.240.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.849
r_dihedral_angle_4_deg21.435
r_dihedral_angle_3_deg15.055
r_long_range_B_refined7.51
r_dihedral_angle_1_deg6.788
r_mcangle_it4.172
r_scbond_it3.982
r_mcbond_it3.064
r_angle_refined_deg1.533
r_chiral_restr0.114
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.849
r_dihedral_angle_4_deg21.435
r_dihedral_angle_3_deg15.055
r_long_range_B_refined7.51
r_dihedral_angle_1_deg6.788
r_mcangle_it4.172
r_scbond_it3.982
r_mcbond_it3.064
r_angle_refined_deg1.533
r_chiral_restr0.114
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2163
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
DIALSdata reduction