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COMPLEX OF DIPHTHERIA TOXIN AND HEPARIN-BINDING EPIDERMAL GROWTH FACTOR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MDT PDB ENTRY 1MDT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 PROTEIN (15 MG/ML) IN 10 MM TRIS-HCL (PH 7.5), 0.15 M NACL MIXED WITH AN EQUAL VOLUME OF PRECIPITANT CONTAINING 50 MM TRIS-HCL (PH 7.5), 0.15 M NACL, 5% (V/V) GLYCEROL, 22-30% (W/V) POLYETHYLENE GLYCOL 3350; AND EQUILIBRATED BY VAPOR DIFFUSION AGAINST PRECIPITANT, vapor diffusion
Crystal Properties Matthews coefficient Solvent content 2.3 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.4 α = 90 b = 103.7 β = 90 c = 127.7 γ = 90
Symmetry Space Group C 2 2 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 MACSCIENCE MIRRORS 1996-10-10 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) R Sym 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 2.65 25 88.5 0.052 0.052 27.9 3.6 54532
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.74 79.2 0.152 0.152 5 2.1
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 THROUGHOUT PDB ENTRY 1MDT 2.65 25 15511 750 88.5 0.172 0.172 0.1831 0.29 RANDOM 37.9
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_scangle_it 7.35 x_scbond_it 5.23 x_mcangle_it 5.21 x_mcbond_it 3.45 x_angle_deg 1.5 x_improper_angle_d 1.34 x_bond_d 0.009 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 24.3 x_scangle_it 7.35 x_scbond_it 5.23 x_mcangle_it 5.21 x_mcbond_it 3.45 x_angle_deg 1.5 x_improper_angle_d 1.34 x_bond_d 0.009 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4306 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing X-PLOR refinement