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NUCLEOTIDE-FREE DIPHTHERIA TOXIN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DDT DT-DIMER APUP COMPLEX (PDB ENTRY 1DDT)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 HANGING DROP, 12 % PEG8000, 0.43M NACL, 0.043M TRIS, PH 7.5, vapor diffusion - hanging drop
Crystal Properties Matthews coefficient Solvent content 2.67 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.2 α = 90 b = 91.2 β = 94.2 c = 65.3 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 94 IMAGE PLATE RIGAKU 1994-04-15 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1
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 2.2 95.7 0.066 9.6 2.8 26627 33.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.4 92.7 0.239 2.6
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-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-FACTOR DT-DIMER APUP COMPLEX (PDB ENTRY 1DDT) 2.3 8 25726 2565 96.2 0.182 0.182 0.184 0.282 RANDOM 38.8
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]
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 24.3 x_angle_deg 1.5 x_improper_angle_d 1.4 x_bond_d 0.01 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 24.3 x_angle_deg 1.5 x_improper_angle_d 1.4 x_bond_d 0.01 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot x_mcbond_it x_mcangle_it x_scbond_it x_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4021 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms
Software Software Software Name Purpose R-AXIS data collection R-AXIS data reduction X-PLOR model building X-PLOR refinement R-AXIS data scaling X-PLOR phasing