2Z3I

Crystal structure of blasticidin S deaminase (BSD) mutant E56Q complexed with substrate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729320% PEG8000, 0.1M SODIUM CACODYLATE, 50MM MAGNESIUM CHROLIDE, 1MM BLASTICIDIN-S, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.652.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.33α = 90
b = 69.578β = 90
c = 145.99γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XUSPring-8BL45XU

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
11.85091.50.05748599

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 1WN51.85046160243691.50.1780.1750.22RANDOM23.57
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]
1.36-0.11-1.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.138
r_dihedral_angle_4_deg16.884
r_dihedral_angle_3_deg13.688
r_dihedral_angle_1_deg5.527
r_scangle_it3.28
r_scbond_it2.206
r_mcangle_it1.524
r_angle_refined_deg1.512
r_mcbond_it0.879
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.138
r_dihedral_angle_4_deg16.884
r_dihedral_angle_3_deg13.688
r_dihedral_angle_1_deg5.527
r_scangle_it3.28
r_scbond_it2.206
r_mcangle_it1.524
r_angle_refined_deg1.512
r_mcbond_it0.879
r_nbtor_refined0.303
r_metal_ion_refined0.267
r_nbd_refined0.218
r_symmetry_vdw_refined0.175
r_symmetry_hbond_refined0.17
r_xyhbond_nbd_refined0.166
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.007
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 Atoms3744
Nucleic Acid Atoms
Solvent Atoms561
Heterogen Atoms144

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling