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Crystal structure of the human tumor necrosis factor in complex with golimumab Fv
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A8M 1A8M, 5B8C experimental model PDB 5B8C 1A8M, 5B8C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M sodium acetate trihydrate pH 4.6, 1.4M sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.96 58.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.64 α = 90 b = 85.3 β = 101.61 c = 135.96 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 6M 2016-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.73 46.25 97.1 0.107 0.127 0.993 9.47 3.428 77915 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.73 2.8 92.8 0.988 1.163 0.539 1.48 3.52
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1A8M, 5B8C 2.727 46.25 1.37 77902 3936 97.11 0.1922 0.19 0.1967 0.2335 0.2362 77.8314
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.068 f_angle_d 0.672 f_chiral_restr 0.047 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18030 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing