2Z3G

Crystal structure of blasticidin S deaminase (BSD)


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, 50MM TRIS, 50MM MAGNESIUM CHLORIDE, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5351.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.116α = 90
b = 68.762β = 90
c = 146.434γ = 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
11.55099.30.07888094

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 1WN51.539.883571441599.70.1750.1740.199RANDOM15.96
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]
0.9-0.79-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.337
r_dihedral_angle_4_deg18.324
r_dihedral_angle_3_deg11.423
r_dihedral_angle_1_deg4.932
r_scangle_it2.729
r_scbond_it1.788
r_angle_refined_deg1.143
r_mcangle_it1.083
r_mcbond_it0.656
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.337
r_dihedral_angle_4_deg18.324
r_dihedral_angle_3_deg11.423
r_dihedral_angle_1_deg4.932
r_scangle_it2.729
r_scbond_it1.788
r_angle_refined_deg1.143
r_mcangle_it1.083
r_mcbond_it0.656
r_nbtor_refined0.3
r_symmetry_vdw_refined0.251
r_nbd_refined0.201
r_xyhbond_nbd_refined0.127
r_symmetry_hbond_refined0.118
r_chiral_restr0.067
r_metal_ion_refined0.052
r_bond_refined_d0.008
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 Atoms3701
Nucleic Acid Atoms
Solvent Atoms759
Heterogen Atoms27

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling