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Crystal structure of blasticidin S deaminase (BSD)
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, 50MM TRIS, 50MM MAGNESIUM CHLORIDE, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.53 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.116 α = 90 b = 68.762 β = 90 c = 146.434 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 1.5 50 99.3 0.078 88094
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 1.5 39.8 83571 4415 99.7 0.175 0.174 0.173 0.199 0.1981 RANDOM 15.96
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.337 r_dihedral_angle_4_deg 18.324 r_dihedral_angle_3_deg 11.423 r_dihedral_angle_1_deg 4.932 r_scangle_it 2.729 r_scbond_it 1.788 r_angle_refined_deg 1.143 r_mcangle_it 1.083 r_mcbond_it 0.656 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.337 r_dihedral_angle_4_deg 18.324 r_dihedral_angle_3_deg 11.423 r_dihedral_angle_1_deg 4.932 r_scangle_it 2.729 r_scbond_it 1.788 r_angle_refined_deg 1.143 r_mcangle_it 1.083 r_mcbond_it 0.656 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.251 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.127 r_symmetry_hbond_refined 0.118 r_chiral_restr 0.067 r_metal_ion_refined 0.052 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 Atoms Number Protein Atoms 3701 Nucleic Acid Atoms Solvent Atoms 759 Heterogen Atoms 27
Software Software Software Name Purpose AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling