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Crystal structure of TNF alpha in complex with compound 4
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 7.5 296 30% (w/v) PEG 1000, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.89 34.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.705 α = 90 b = 81.592 β = 90 c = 92.277 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 DECTRIS PILATUS 6M 2017-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
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 1.849 61.125 95.3 0.998 9.9 6 33118
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 1.849 1.881 0.371
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 1.849 61.12 32687 1633 94 0.2141 0.2124 0.2248 0.2451 0.2642 RANDOM 47.42
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] -20.678 7.9021 12.7759
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.88 t_omega_torsion 3.55 t_angle_deg 0.99 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 3161 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 32
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction autoPROC data scaling MOLREP phasing