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Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the gp41 FP-MPER Hyb3K construct 514GIGALFLGFLGAAGS528KK-Ahx-655KNEQELLELDKWASLWN671 soaked in PEG/2-propanol solution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 Crystals grown in 0.1 M Nacitrate pH 5.6, 1.6 M ammonium sulfate, 0.01% Tween-20 and soaked for 36h in 0.1 M Nacitrate pH 5.6, 16% PEG 4K, 16% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 43.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.5 α = 90 b = 76.6 β = 90 c = 94.2 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 RIGAKU RAXIS IV++ 2007-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 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 2 20 97.9 0.098 3.5 31694 31016 16.2
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 1.99 2.11 96.1 0.454 1.7
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 3D0L 2 19.9 31694 31016 1550 97.7 0.227 0.227 0.2246 0.254 0.2515 RANDOM 26.5
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] 1.78 0.31 -2.1
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 29 c_scangle_it 2.78 c_mcangle_it 2.03 c_scbond_it 1.99 c_angle_deg 1.7 c_mcbond_it 1.26 c_improper_angle_d 1.02 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3327 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 6
Software Software Software Name Purpose CNS refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling CNS phasing