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Crystal structure of the cholera toxin-like B-subunit from Citrobacter freundii to 1.9 angstrom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EFX PDB ENTRY 3EFX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 10% PEG 6K, 1 M LITHIUM CHLORIDE AND 100 MM SODIUM ACETATE PH 4.6. 20% GLYECROL WERE ADDED AS CRYOPROTECTANT
Crystal Properties Matthews coefficient Solvent content 1.98 37.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.05 α = 90 b = 100.94 β = 122.24 c = 83.27 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 100 CCD ADSC CCD 2007-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 1.895 43.9 98.4 0.05 13.1 3.7 71465 2 18.9
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 1.89 2 89.1 0.26 2.9 2.9
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 3EFX 1.895 40.9 67864 3600 98.31 0.17551 0.17364 0.177 0.21121 0.2138 RANDOM 16.686
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] -0.46 -0.55 -0.54 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.043 r_dihedral_angle_3_deg 16.075 r_dihedral_angle_4_deg 15.258 r_dihedral_angle_1_deg 6.398 r_scangle_it 4.429 r_scbond_it 2.71 r_mcangle_it 1.961 r_angle_refined_deg 1.538 r_mcbond_it 1.075 r_angle_other_deg 0.945
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.043 r_dihedral_angle_3_deg 16.075 r_dihedral_angle_4_deg 15.258 r_dihedral_angle_1_deg 6.398 r_scangle_it 4.429 r_scbond_it 2.71 r_mcangle_it 1.961 r_angle_refined_deg 1.538 r_mcbond_it 1.075 r_angle_other_deg 0.945 r_mcbond_other 0.253 r_chiral_restr 0.094 r_bond_refined_d 0.017 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 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_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 7427 Nucleic Acid Atoms Solvent Atoms 512 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing