2Z3J

Crystal structure of blasticidin S deaminase (BSD) R90K mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WN5PDB ENTRY 1WN5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729820% PEG8000, 50MM MAGNESIUM CHLORIDE, 0.1M SODIUM CACODYLATE,, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.652.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.802α = 90
b = 69.952β = 90
c = 145.844γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 210MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B1SPring-8BL26B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.65099.90.06374806

Refinement

Statistics
Diffraction IDStructure Solution 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 REPLACEMENTPDB ENTRY 1WN51.643.8169253368597.50.1860.1850.214RANDOM19.27
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]
1.36-0.66-0.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.163
r_dihedral_angle_4_deg17.985
r_dihedral_angle_3_deg12.007
r_dihedral_angle_1_deg5.204
r_scangle_it3.224
r_scbond_it2.037
r_mcangle_it1.271
r_angle_refined_deg1.192
r_mcbond_it0.756
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.163
r_dihedral_angle_4_deg17.985
r_dihedral_angle_3_deg12.007
r_dihedral_angle_1_deg5.204
r_scangle_it3.224
r_scbond_it2.037
r_mcangle_it1.271
r_angle_refined_deg1.192
r_mcbond_it0.756
r_nbtor_refined0.298
r_nbd_refined0.205
r_symmetry_vdw_refined0.171
r_xyhbond_nbd_refined0.122
r_symmetry_hbond_refined0.102
r_metal_ion_refined0.085
r_chiral_restr0.071
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3638
Nucleic Acid Atoms
Solvent Atoms468
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling