☰ Navigation Tabs
Crystal structure of blasticidin S deaminase (BSD) R90K mutant
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 7 298 20% PEG8000, 50MM MAGNESIUM CHLORIDE, 0.1M SODIUM CACODYLATE,, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.6 52.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.802 α = 90 b = 69.952 β = 90 c = 145.844 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 CCD RIGAKU JUPITER 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 SPring-8 BL26B1
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 1.6 50 99.9 0.063 74806
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 1.6 43.81 69253 3685 97.5 0.186 0.185 0.1842 0.214 0.2121 RANDOM 19.27
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.163 r_dihedral_angle_4_deg 17.985 r_dihedral_angle_3_deg 12.007 r_dihedral_angle_1_deg 5.204 r_scangle_it 3.224 r_scbond_it 2.037 r_mcangle_it 1.271 r_angle_refined_deg 1.192 r_mcbond_it 0.756 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.163 r_dihedral_angle_4_deg 17.985 r_dihedral_angle_3_deg 12.007 r_dihedral_angle_1_deg 5.204 r_scangle_it 3.224 r_scbond_it 2.037 r_mcangle_it 1.271 r_angle_refined_deg 1.192 r_mcbond_it 0.756 r_nbtor_refined 0.298 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.122 r_symmetry_hbond_refined 0.102 r_metal_ion_refined 0.085 r_chiral_restr 0.071 r_bond_refined_d 0.011 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 3638 Nucleic Acid Atoms Solvent Atoms 468 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling