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Crystal structure of the therapeutical antibody fragment of canakinumab in its unbound state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PZ5 1PZ5 and 3BKJ experimental model PDB 3BKJ 1PZ5 and 3BKJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 crystal grown in 11% w/v PEG 3350 and 0.14M Tris-HCL equilibrated against a reservoir solution of 24% w/v PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.24 45.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.216 α = 90 b = 54.585 β = 90 c = 94.088 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 2011-10-14 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 1.8 94.1 75 0.104 0.113 6.6 250861 37442 2 2 16.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 99.4 3.9 6.5
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 1PZ5 and 3BKJ 1.83 40 37442 37375 1869 99.36 0.1948 0.1933 0.1993 0.2222 0.2287 RANDOM 19.39
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] -1.391 1.628 -0.237
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.64 t_omega_torsion 2.94 t_angle_deg 1.01 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.64 t_omega_torsion 2.94 t_angle_deg 1.01 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3273 Nucleic Acid Atoms Solvent Atoms 445 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