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Crystal structure of TNF alpha in complex with compound 3.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9OJO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 296 20% (w/v) PEG 3000, 0.1M Tris pH 7.0, 0.2M calcium acetate.
Crystal Properties Matthews coefficient Solvent content 2.13 42.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 251.546 α = 90 b = 65.589 β = 95.08 c = 54.416 γ = 90
Symmetry Space Group C 1 2 1
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 DECTRIS PILATUS 6M 2017-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.158 125.28 100 0.954 2.8 3.4 47741
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.158 2.195 0.346
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 2.158 125.28 44807 2204 93.8 0.2169 0.215 0.2339 0.2532 0.2784 RANDOM 84.63
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] 6.264 2.7388 -12.9624 6.6985
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.26 t_omega_torsion 2.94 t_angle_deg 0.95 t_bond_d 0.008 t_dihedral_angle_d 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 5990 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 70
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction autoPROC data scaling MOLREP phasing