☰ Navigation Tabs
Crystal structure of blasticidin S deaminase (BSD) complexed with deaminohydroxy blasticidin S
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 CHLORIDE, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.55 51.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.3 α = 90 b = 69.275 β = 90 c = 146.535 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 99.8 0.091 89147
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1WN5 1.5 50 84565 4460 99.8 0.173 0.172 0.185 0.1897 RANDOM 14.88
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] 0.64 -0.43 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.726 r_dihedral_angle_4_deg 18.651 r_dihedral_angle_3_deg 11.762 r_dihedral_angle_1_deg 5.066 r_scangle_it 2.713 r_scbond_it 1.646 r_angle_refined_deg 1.229 r_mcangle_it 1.058 r_mcbond_it 0.61 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.726 r_dihedral_angle_4_deg 18.651 r_dihedral_angle_3_deg 11.762 r_dihedral_angle_1_deg 5.066 r_scangle_it 2.713 r_scbond_it 1.646 r_angle_refined_deg 1.229 r_mcangle_it 1.058 r_mcbond_it 0.61 r_nbtor_refined 0.301 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.123 r_symmetry_hbond_refined 0.104 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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_refined 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 3703 Nucleic Acid Atoms Solvent Atoms 686 Heterogen Atoms 124
Software Software Software Name Purpose AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling