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Crystal structure of the complex between CNTO607 Fab and IL-13
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G6A PDB entries 3G6A, 1IJZ experimental model PDB 1IJZ PDB entries 3G6A, 1IJZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 293 0.1 M Sodium acetate pH 4.5, 4.9 M Sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.5 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.54 α = 90 b = 68.03 β = 90 c = 182.35 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 115 CCD RIGAKU SATURN 944 VARIMAX HF 2006-12-22 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 3.2 63 91.5 0.161 6.1 6 13028 -3 19.5
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 3.2 3.31 88.2 0.22 4.6 2.5
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 (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 entries 3G6A, 1IJZ 3.2 15 16206 12362 501 100 0.213 0.213 0.2128 0.26342 0.2463 RANDOM 18.7
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] -1.18 2.76 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.716 r_scangle_it 26.417 r_dihedral_angle_4_deg 20.4 r_scbond_it 20.351 r_dihedral_angle_3_deg 20.079 r_dihedral_angle_1_deg 6.704 r_mcangle_it 4.75 r_mcbond_it 1.387 r_angle_refined_deg 1.361 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.716 r_scangle_it 26.417 r_dihedral_angle_4_deg 20.4 r_scbond_it 20.351 r_dihedral_angle_3_deg 20.079 r_dihedral_angle_1_deg 6.704 r_mcangle_it 4.75 r_mcbond_it 1.387 r_angle_refined_deg 1.361 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.297 r_nbd_refined 0.239 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.086 r_symmetry_hbond_refined 0.074 r_bond_refined_d 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_refined r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4054 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 5
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement d*TREK data reduction