8PNW

Crystal structure of D-amino acid aminotransferase from Blastococcus saxobsidens in holo form with PLP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Q1R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2880.1 M Hepes pH 7.5, 4 M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.8657.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.935α = 90
b = 105.935β = 90
c = 51.324γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.96770ESRFID23-1

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
11.752.9797.40.0830.0980.0510.99410.13.535723
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)
11.71.7391.50.4810.5860.330.7922.8

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 REPLACEMENTTHROUGHOUT1.752.9734008170097.250.1720.170940.19246RANDOM22.373
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]
0.540.270.54-1.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.562
r_dihedral_angle_4_deg14.95
r_dihedral_angle_3_deg13.278
r_dihedral_angle_1_deg6.042
r_long_range_B_refined5.061
r_long_range_B_other4.96
r_scangle_other4.095
r_scbond_other2.802
r_scbond_it2.798
r_mcangle_it2.597
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.562
r_dihedral_angle_4_deg14.95
r_dihedral_angle_3_deg13.278
r_dihedral_angle_1_deg6.042
r_long_range_B_refined5.061
r_long_range_B_other4.96
r_scangle_other4.095
r_scbond_other2.802
r_scbond_it2.798
r_mcangle_it2.597
r_mcangle_other2.597
r_mcbond_it1.821
r_mcbond_other1.818
r_angle_refined_deg1.686
r_angle_other_deg1.494
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms2020
Nucleic Acid Atoms
Solvent Atoms305
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction