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Complex between human TNF alpha and Llama VHH2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 to 300 nL of protein at 11 mg per ml in HEPES 10 mM pH 7.0 with 100 nL of precipitant solution containing 12% 130 mM NaCl and 366 mM CaCl2 and 70 mM CAPS pH 9.0 and 30 mM MES pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.3 46.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.31 α = 90 b = 87.31 β = 90 c = 62.73 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2005-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.931 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 48.3 97.9 0.035 0.999 23.5 2.9 21089 15.63
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 94.6 0.1 0.98 11 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5M2I 1.9 48.28 21089 1045 97.86 0.1602 0.1583 0.1615 0.1962 0.1997 RANDOM 19.78
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] 0.267 0.267 -0.5341
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.9 t_omega_torsion 3.91 t_angle_deg 1.11 t_bond_d 0.01 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 17.9 t_omega_torsion 3.91 t_angle_deg 1.11 t_bond_d 0.01 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 1966 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling MOLREP phasing