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Crystal structure of the HIV-1 Cross Neutralizing Antibody 2F5 in complex with gp41 Peptide ELLELDKWASLWN grown in ammonium sulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P8M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 Fab fragment and peptide are incubated in a solution containing 0.01% Tween-20. Crystals are obatined from reservoir solution containing 0.1 M Nacitrate pH 5.6, 1.6 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.9 α = 90 b = 76.5 β = 90 c = 93.9 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 IMAGE PLATE MAR scanner 345 mm plate 2008-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.9 17 93.7 0.282 6.01 4436 4156
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.9 4.14 90.9 0.514 5.69
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 MOLECULAR REPLACEMENT THROUGHOUT 2P8M 3.9 16.96 4436 4156 209 93.6 0.222 0.222 0.2268 0.263 0.2645 RANDOM 34.6
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] -4.69 6.06 -1.37
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 29.5 c_scangle_it 3.47 c_mcangle_it 2.76 c_scbond_it 2.41 c_angle_deg 2.1 c_mcbond_it 1.7 c_improper_angle_d 1.45 c_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3321 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose CNS refinement MAR345dtb data collection XDS data reduction XDS data scaling CNS phasing