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Structure of a mutant Cetuximab Fab fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YY8 PDB entry 1YY8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100 mM sodium citrate, 1.6 M ammonium sulfate, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 2.99 58.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.06 α = 90 b = 83.07 β = 90 c = 211.6 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 CCD ADSC QUANTUM 315r 2014-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 47.42 99.7 0.999 16.2 6.7 124960
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 1YY8 1.7 47.42 118489 6362 99.92 0.17284 0.17157 0.1805 0.19707 0.2053 RANDOM 25.786
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] -0.68 1.69 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.321 r_dihedral_angle_4_deg 18.516 r_dihedral_angle_3_deg 11.53 r_dihedral_angle_1_deg 7.856 r_long_range_B_refined 5.042 r_long_range_B_other 5.042 r_scangle_other 2.423 r_mcangle_it 1.983 r_mcangle_other 1.983 r_angle_refined_deg 1.556
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.321 r_dihedral_angle_4_deg 18.516 r_dihedral_angle_3_deg 11.53 r_dihedral_angle_1_deg 7.856 r_long_range_B_refined 5.042 r_long_range_B_other 5.042 r_scangle_other 2.423 r_mcangle_it 1.983 r_mcangle_other 1.983 r_angle_refined_deg 1.556 r_scbond_it 1.516 r_scbond_other 1.516 r_mcbond_it 1.209 r_mcbond_other 1.209 r_angle_other_deg 0.937 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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 6544 Nucleic Acid Atoms Solvent Atoms 856 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing