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Crystal structure of the A-subunit of the AB5 toxin from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MEE PDB ENTRY 1MEE
Crystallization Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.967 α = 90 b = 78.987 β = 90 c = 95.782 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 RAXIS MIRRORS 2005-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 1.8 35 99 0.05 15 2.1 31757
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 1.8 1.85 88 0.15 2 2
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 PDB ENTRY 1MEE 1.8 30 30146 1609 98.3 0.2 0.2 0.2078 0.23 0.2295 RANDOM 29.31
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] -0.69 -1.36 2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.366 r_dihedral_angle_4_deg 15.392 r_dihedral_angle_3_deg 12.982 r_dihedral_angle_1_deg 5.654 r_scangle_it 2.599 r_scbond_it 1.648 r_angle_refined_deg 1.199 r_mcangle_it 0.949 r_mcbond_it 0.568 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.366 r_dihedral_angle_4_deg 15.392 r_dihedral_angle_3_deg 12.982 r_dihedral_angle_1_deg 5.654 r_scangle_it 2.599 r_scbond_it 1.648 r_angle_refined_deg 1.199 r_mcangle_it 0.949 r_mcbond_it 0.568 r_nbtor_refined 0.305 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.176 r_symmetry_hbond_refined 0.157 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.079 r_bond_refined_d 0.009 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_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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2320 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing