☰ Navigation Tabs
First Crystal Structure of E.coli Based Recombinant Diphtheria Toxin Mutant CRM197
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AE1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 292 Protein: 22.9 mg/ml, 0.15M Sodium chloride,0.01M Tris-HCL (pH 8.3);
Screen: Classics II (G2), 0.2M Lithium sulfate, 0.1M Bis-Tris (pH 5.5), 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.52 51.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.214 α = 90.09 b = 69.167 β = 90.01 c = 127.882 γ = 82.02
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 MARMOSAIC 225 mm CCD 2015-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.35 30 98.4 0.051 0.051 18.2 2.6 98137 -3 57.5
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 2.35 2.39 97.7 0.424 2.3 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4AE1 2.35 29.08 91347 4932 98.39 0.20958 0.20722 0.2071 0.25026 0.2483 RANDOM 66.023
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] 1.84 -1.35 1.23 -1.5 -2.22 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.222 r_dihedral_angle_3_deg 8.712 r_long_range_B_refined 7.01 r_long_range_B_other 7.01 r_dihedral_angle_4_deg 6.066 r_scangle_other 4.263 r_mcangle_other 3.505 r_mcangle_it 3.504 r_scbond_it 2.676 r_scbond_other 2.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.222 r_dihedral_angle_3_deg 8.712 r_long_range_B_refined 7.01 r_long_range_B_other 7.01 r_dihedral_angle_4_deg 6.066 r_scangle_other 4.263 r_mcangle_other 3.505 r_mcangle_it 3.504 r_scbond_it 2.676 r_scbond_other 2.676 r_dihedral_angle_1_deg 2.429 r_mcbond_it 2.3 r_mcbond_other 2.298 r_angle_refined_deg 1.174 r_angle_other_deg 0.669 r_chiral_restr 0.069 r_gen_planes_refined 0.019 r_gen_planes_other 0.016 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15714 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement BLU-MAX data collection HKL-3000 data reduction HKL-3000 data scaling PHASER phasing