☰ Navigation Tabs
Crystal structure of human TNF alpha in complex with TNF30(VHH) domain of ozoralizumab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M2J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 0.03M Diethylene glycol; 0.03M Triethylene glycol; 0.03M Tetraethylene glycol; 0.03M Pentaethylene glycol
0.05M Sodium HEPES; 0.05M MOPS pH7.5
12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.44 49.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.03 α = 90 b = 121.16 β = 94.58 c = 123.61 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 EIGER X 9M 2023-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.00000 SPring-8 BL32XU
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 2.59 45.79 99.3 0.991 7.32 4.2 50898
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 2.59 2.75 0.531
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 2.59 45.79 48495 2381 99.31 0.2112 0.20851 0.2124 0.26876 0.2649 RANDOM 76.882
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] -0.98 -1.74 4.21 -2.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.013 r_dihedral_angle_4_deg 20.634 r_long_range_B_refined 17.182 r_long_range_B_other 17.182 r_dihedral_angle_3_deg 16.268 r_mcangle_it 10.717 r_mcangle_other 10.717 r_scangle_other 10.002 r_dihedral_angle_1_deg 7.372 r_mcbond_it 6.819
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.013 r_dihedral_angle_4_deg 20.634 r_long_range_B_refined 17.182 r_long_range_B_other 17.182 r_dihedral_angle_3_deg 16.268 r_mcangle_it 10.717 r_mcangle_other 10.717 r_scangle_other 10.002 r_dihedral_angle_1_deg 7.372 r_mcbond_it 6.819 r_mcbond_other 6.818 r_scbond_it 6.354 r_scbond_other 6.353 r_angle_refined_deg 1.472 r_angle_other_deg 1.166 r_chiral_restr 0.054 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12084 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing