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Crystal Structure of 3BD10: A Monoclonal Antibody against the TSH Receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K23 PDB ENTRY 4K23
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.4 291 20mM Tris.HCl, 11% PEG4K, pH 7.4, EVAPORATION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.4 48.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.979 α = 90 b = 136.979 β = 90 c = 149.071 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 IMAGE PLATE RIGAKU RAXIS IV++ 2013-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.5 100.86 99.8 0.11 7.6 8.9 32117 2 24.7
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 2.5 2.6 100 0.626 1.7 9.1 32620
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 4K23 2.5 100.86 30401 30401 1623 99.53 0.23766 0.23766 0.23547 0.2407 0.2785 0.2795 RANDOM 38.948
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] -0.75 -4.83 5.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.184 r_dihedral_angle_4_deg 18.526 r_dihedral_angle_3_deg 16.538 r_dihedral_angle_1_deg 6.584 r_long_range_B_refined 6.428 r_long_range_B_other 6.424 r_scangle_other 4.053 r_mcangle_it 3.871 r_mcangle_other 3.871 r_angle_other_deg 3.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.184 r_dihedral_angle_4_deg 18.526 r_dihedral_angle_3_deg 16.538 r_dihedral_angle_1_deg 6.584 r_long_range_B_refined 6.428 r_long_range_B_other 6.424 r_scangle_other 4.053 r_mcangle_it 3.871 r_mcangle_other 3.871 r_angle_other_deg 3.682 r_scbond_it 2.482 r_scbond_other 2.482 r_mcbond_it 2.371 r_mcbond_other 2.371 r_angle_refined_deg 1.491 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6478 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing REFMAC refinement XDS data reduction Aimless data scaling