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Structure of Epa1A in complex with the T-antigen (Gal-b1-3- GalNAc)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other EPA1A WILD TYPE, COMPLEXED WITH LACTOSE CONTAMINANT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 0.1M MES PH6.5 0.2M AMMOMIUM SULFATE 25% PEG 5000 MME 0.025 M LACTOSE
Crystal Properties Matthews coefficient Solvent content 2.31 46.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.6 α = 89.9 b = 103.9 β = 90 c = 69.4 γ = 89.9
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 CCD MARRESEARCH MIRRORS 2012-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.24 10 98.7 0.03 22.7 4.1 75251 -3
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 1.24 1.31 97.5 0.55 2.7 4.1
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT EPA1A WILD TYPE, COMPLEXED WITH LACTOSE CONTAMINANT 1.24 10 72672 2579 98.49 0.11864 0.11733 0.1352 0.15521 0.1718 RANDOM 14.974
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] -0.58 0.96 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.63 r_dihedral_angle_3_deg 13.991 r_dihedral_angle_4_deg 12.496 r_dihedral_angle_1_deg 7.082 r_scangle_it 5.506 r_mcangle_it 4.564 r_scbond_it 3.886 r_mcbond_it 3.081 r_rigid_bond_restr 1.746 r_angle_refined_deg 1.524
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.63 r_dihedral_angle_3_deg 13.991 r_dihedral_angle_4_deg 12.496 r_dihedral_angle_1_deg 7.082 r_scangle_it 5.506 r_mcangle_it 4.564 r_scbond_it 3.886 r_mcbond_it 3.081 r_rigid_bond_restr 1.746 r_angle_refined_deg 1.524 r_mcbond_other 0.906 r_angle_other_deg 0.845 r_chiral_restr 0.054 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1820 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling XSCALE data scaling REFMAC phasing