9S1P | pdb_00009s1p

Crystal structure of the DABA transaminase EctB from the halophilic and cold-adapted Marinobacter sp. CK1 -Mutant K264A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52770.1M bisTRIS propane pH 7.5 0.1M disodium malonate 25% PEG3350 (w/v)
Crystal Properties
Matthews coefficientSolvent content
2.5952.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.027α = 90
b = 79.893β = 90
c = 180.161γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2023-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91840BESSY14.1

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
11.5548.051000.018121.31.970422
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)
11.551.581000.2420.8883.11.9

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 REPLACEMENTTHROUGHOUT1.5548.0566855356599.940.139310.138070.15160.163350.1736RANDOM20.263
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]
1.51-0.33-1.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.623
r_dihedral_angle_2_deg9.581
r_dihedral_angle_1_deg6.331
r_long_range_B_refined6.109
r_long_range_B_other5.791
r_scangle_other4.89
r_scbond_it3.348
r_scbond_other3.274
r_mcangle_other2.289
r_mcangle_it2.288
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.623
r_dihedral_angle_2_deg9.581
r_dihedral_angle_1_deg6.331
r_long_range_B_refined6.109
r_long_range_B_other5.791
r_scangle_other4.89
r_scbond_it3.348
r_scbond_other3.274
r_mcangle_other2.289
r_mcangle_it2.288
r_angle_refined_deg2.017
r_mcbond_it1.619
r_mcbond_other1.603
r_angle_other_deg0.686
r_chiral_restr0.101
r_bond_refined_d0.012
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 Atoms3193
Nucleic Acid Atoms
Solvent Atoms402
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing