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Crystal structure of blasticidin S deaminase (BSD) mutant E56Q complexed with substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WN5 PDB ENTRY 1WN5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 20% PEG8000, 0.1M SODIUM CACODYLATE, 50MM MAGNESIUM CHROLIDE, 1MM BLASTICIDIN-S, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.33 α = 90 b = 69.578 β = 90 c = 145.99 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 50 91.5 0.057 48599
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1WN5 1.8 50 46160 2436 91.5 0.178 0.175 0.174 0.22 0.2173 RANDOM 23.57
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.138 r_dihedral_angle_4_deg 16.884 r_dihedral_angle_3_deg 13.688 r_dihedral_angle_1_deg 5.527 r_scangle_it 3.28 r_scbond_it 2.206 r_mcangle_it 1.524 r_angle_refined_deg 1.512 r_mcbond_it 0.879 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.138 r_dihedral_angle_4_deg 16.884 r_dihedral_angle_3_deg 13.688 r_dihedral_angle_1_deg 5.527 r_scangle_it 3.28 r_scbond_it 2.206 r_mcangle_it 1.524 r_angle_refined_deg 1.512 r_mcbond_it 0.879 r_nbtor_refined 0.303 r_metal_ion_refined 0.267 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.175 r_symmetry_hbond_refined 0.17 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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 Atoms Number Protein Atoms 3744 Nucleic Acid Atoms Solvent Atoms 561 Heterogen Atoms 144
Software Software Software Name Purpose AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling