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Crystal structure of the mAb 15A in complex with COMP-epitope P6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IQW 1IQW, 2IPT experimental model PDB 2IPT 1IQW, 2IPT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 30% polyethylene glycol 8000, 0.2 M ammonium sulphate
10 mg/ml 15A Fab fragment + P6 peptide (molar ratio 1:1.2) in 20 mM Tris HCl pH 7.4, 50 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.62 53.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.174 α = 90 b = 84.421 β = 90 c = 151.885 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 PILATUS 6M 2014-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.9 84.42 98.9 0.062 0.071 0.034 0.998 12.6 3.9 80712
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 99.3 0.539 0.617 0.292 0.731 3.9
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 1IQW, 2IPT 1.9 84 76757 3924 98.5 0.1752 0.1738 0.1814 0.2031 0.2078 RANDOM 37.924
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] -0.32 -1.44 1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.827 r_dihedral_angle_4_deg 16.092 r_dihedral_angle_3_deg 12.809 r_dihedral_angle_1_deg 6.203 r_angle_refined_deg 1.301 r_angle_other_deg 0.95 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.827 r_dihedral_angle_4_deg 16.092 r_dihedral_angle_3_deg 12.809 r_dihedral_angle_1_deg 6.203 r_angle_refined_deg 1.301 r_angle_other_deg 0.95 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6892 Nucleic Acid Atoms Solvent Atoms 608 Heterogen Atoms 46
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction PHASER phasing