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CRYSTAL STRUCTURE OF THE ADCC-POTENT, WEAKLY NEUTRALIZING HIV ENV CO-RECEPTOR BINDING SITE ANTIBODY N12-I2 FAB IN COMPLEX WITH HIV-1 CLADE A/E GP120 AND M48U1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UWE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 15% PEG 6000
5% MPD
0.1 M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.14 42.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.687 α = 90 b = 69.522 β = 90 c = 213.468 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 PIXEL DECTRIS PILATUS 6M 2016-01-07 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 325 mm CCD 2016-01-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2 2 SYNCHROTRON SSRL BEAMLINE BL14-1 0.97946 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 3.2 50 88.5 0.321 0.156 0.931 6.3 4.3 12129
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.26 66.9 0.521 0.434 0.611 1.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5UWE 3.2 42.34 1.35 12090 612 88.49 0.2439 0.241 0.2437 0.3011 0.2972
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.199 f_angle_d 0.686 f_chiral_restr 0.047 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6194 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 126
Software Software Software Name Purpose PHENIX refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing