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Crystal Structure of the broadly neutralizing anti-HIV-1 antibody 2F5 in complex with a gp41 17mer epitope
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TJH PDB ENTRY 1TJH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 293 20% PEG 4000, 20% Isopropanol, 0.125 M NaCitrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.60
Crystal Properties Matthews coefficient Solvent content 3.296 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.66 α = 90 b = 63.684 β = 90 c = 178.375 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 CCD MARRESEARCH 2003-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.2 50 96 0.126 14.5 6.2 32958 -3 22.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.28 75.5 0.494 1.95 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 DIFFERENCE FOURIER METHOD THROUGHOUT PDB ENTRY 1TJH 2.2 20 46092 30875 3104 89.3 0.183 0.183 0.1799 0.221 0.22 RANDOM 36.1
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] 3.44 -2.94 -0.51
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 27 c_scangle_it 3.18 c_mcangle_it 2.32 c_scbond_it 2.17 c_angle_deg 1.4 c_mcbond_it 1.4 c_improper_angle_d 0.83 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 27 c_scangle_it 3.18 c_mcangle_it 2.32 c_scbond_it 2.17 c_angle_deg 1.4 c_mcbond_it 1.4 c_improper_angle_d 0.83 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3546 Nucleic Acid Atoms Solvent Atoms 577 Heterogen Atoms 12
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing