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Structure of IL-13 antibody H2L6, A humanized variant OF C836
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L5X PDB ENTRY 3L5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M MES PH 6.5, 5% PEG 4K, 38% MPD;
CRYO CONDITIONS: 0.1 M MES PH 6.5, 5% PEG 4K, 40% MPD, 15% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.26 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.64 α = 90 b = 228.16 β = 90 c = 234 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD RIGAKU SATURN 944 VARIMAX HF 2008-01-04 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 2.6 66.6 97.1 0.087 9.6 7 56212 56212 -3 56.8
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) 2.6 2.69 92.8 0.42 2.3 4.5
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 3L5X 2.6 15 53577 53577 2269 93 0.20667 0.20667 0.20514 0.207 0.24264 0.2435 RANDOM 52.7
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] -0.03 0.05 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.114 r_dihedral_angle_4_deg 22.683 r_scangle_it 19.22 r_scbond_it 18.788 r_dihedral_angle_3_deg 18.076 r_dihedral_angle_1_deg 6.823 r_mcangle_it 5.156 r_mcbond_it 2.933 r_angle_refined_deg 1.352 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.114 r_dihedral_angle_4_deg 22.683 r_scangle_it 19.22 r_scbond_it 18.788 r_dihedral_angle_3_deg 18.076 r_dihedral_angle_1_deg 6.823 r_mcangle_it 5.156 r_mcbond_it 2.933 r_angle_refined_deg 1.352 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.221 r_symmetry_vdw_refined 0.217 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9959 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 16
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement d*TREK data reduction d*TREK data scaling