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The structure of an antitumor CH2-domain-deleted humanized antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BBJ PDB ENTRY 1BBJ; PDB ENTRY 1FC1 experimental model PDB 1FC1 PDB ENTRY 1BBJ; PDB ENTRY 1FC1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 290 4 M sodium formate, 1.5 mM Triton X-100 detergent, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.20
Crystal Properties Matthews coefficient Solvent content 3.29 62.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.54 α = 90 b = 224.2 β = 90 c = 166.59 γ = 90
Symmetry Space Group P 21 21 2
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 4 2003-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 ALS 5.0.2
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 2.8 45.13 99.9 0.152 10.9 9.06 76662 22.7
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) 2.8 2.9 98 0.365 5 7.62
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 1BBJ;
PDB ENTRY 1FC1 2.8 45.13 4 76929 76662 5924 99.5 0.246 0.246 0.2458 0.296 0.2974 RANDOM 41.4
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] 16.32 -3.31 -13.01
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 27.3 c_mcangle_it 2.42 c_scangle_it 2.39 c_angle_deg 1.88 c_scbond_it 1.52 c_mcbond_it 1.38 c_improper_angle_d 1.32 c_bond_d 0.013 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 27.3 c_mcangle_it 2.42 c_scangle_it 2.39 c_angle_deg 1.88 c_scbond_it 1.52 c_mcbond_it 1.38 c_improper_angle_d 1.32 c_bond_d 0.013 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16740 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose CNS refinement d*TREK data reduction d*TREK data scaling CNS phasing