9S1Q | pdb_00009s1q

Crystal structure of the DABA transaminase EctB from the halophilic and cold-adapted Marinobacter sp. CK1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6RL5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82770.1M bisTRIS propane pH 8, 0.2 M disodium malonate, 19.6 % PEG3350 (w/v).
Crystal Properties
Matthews coefficientSolvent content
2.3447.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.648α = 90
b = 99.332β = 104.82
c = 112.698γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2022-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.87313ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
1245.5399.60.0890.9915.81.9115468
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0399.70.7730.45111.9

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT240.13109707573699.550.167520.16540.1730.208150.214RANDOM38.475
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]
-1.550.670.640.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg15.819
r_dihedral_angle_3_deg13.462
r_long_range_B_refined6.988
r_long_range_B_other6.966
r_dihedral_angle_1_deg6.677
r_scangle_other6.14
r_scbond_it4.372
r_scbond_other4.372
r_mcangle_it3.621
r_mcangle_other3.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg15.819
r_dihedral_angle_3_deg13.462
r_long_range_B_refined6.988
r_long_range_B_other6.966
r_dihedral_angle_1_deg6.677
r_scangle_other6.14
r_scbond_it4.372
r_scbond_other4.372
r_mcangle_it3.621
r_mcangle_other3.62
r_mcbond_it2.897
r_mcbond_other2.897
r_angle_refined_deg2.177
r_angle_other_deg0.74
r_chiral_restr0.115
r_bond_refined_d0.014
r_gen_planes_refined0.01
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 Atoms12768
Nucleic Acid Atoms
Solvent Atoms641
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction