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Crystal structure of EpCAM in complex with scFv
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SVZ 1SVZ, 4MZV experimental model PDB 4MZV 1SVZ, 4MZV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 6.4 293 0.1 M PCTP pH 6.4, 21 % w/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.97 58.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.886 α = 90 b = 91.071 β = 90 c = 181.445 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 PIXEL DECTRIS PILATUS3 S 6M 2015-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 28.7 99.2 0.061 0.999 14.7 4.8 56398 53.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.42 98 1.175 0.514 1.1 4.6
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 1SVZ, 4MZV 2.35 28.7 53487 2851 99.2 0.23267 0.23016 0.2349 0.27876 0.2833 RANDOM 87.131
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] -2.16 0.37 1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.077 r_dihedral_angle_3_deg 16.06 r_dihedral_angle_4_deg 15.699 r_long_range_B_refined 12.145 r_long_range_B_other 12.144 r_mcangle_it 9.135 r_mcangle_other 9.134 r_scangle_other 8.279 r_dihedral_angle_1_deg 7.975 r_mcbond_it 5.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.077 r_dihedral_angle_3_deg 16.06 r_dihedral_angle_4_deg 15.699 r_long_range_B_refined 12.145 r_long_range_B_other 12.144 r_mcangle_it 9.135 r_mcangle_other 9.134 r_scangle_other 8.279 r_dihedral_angle_1_deg 7.975 r_mcbond_it 5.928 r_mcbond_other 5.927 r_scbond_it 5.28 r_scbond_other 5.28 r_angle_refined_deg 1.418 r_angle_other_deg 1.183 r_chiral_restr 0.051 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7118 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing