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Crystal structure of human IL-1beta in complex with the therapeutic antibody binding fragment of canakinumab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PZ5 1PZ5, 3BKJ, 1TOO experimental model PDB 3BKJ 1PZ5, 3BKJ, 1TOO experimental model PDB 1TOO 1PZ5, 3BKJ, 1TOO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 17.2% w/v PEG 3350 and 0.14M tri-sodium citrate, 24% w/v PEG 3350, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.061 α = 90 b = 37.3 β = 90 c = 189.418 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 PSI PILATUS 6M 2012-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.91 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 94.7 98.8 0.108 0.12 12.1 5.3 207933 38275 2 2 29.23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 93.5 0.108 0.12 2.3 5.3 37806
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 1PZ5, 3BKJ, 1TOO 2.03 39.36 2 37806 37684 1891 98.59 0.227 0.2257 0.2247 0.2519 0.2542 RANDOM 35.92
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] -7.0896 -0.8482 7.9378
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.04 t_omega_torsion 2.51 t_angle_deg 1.02 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4466 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms
Software Software Software Name Purpose XDS data scaling autoPROC data collection PHASER phasing BUSTER refinement XDS data reduction autoPROC data scaling SCALA data scaling