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Crystal structure of 10E8 Fab light chain mutant3, against the MPER region of the HIV-1 Env, in complex with the MPER epitope scaffold T117v2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G6F 4G6F, 3LF6 experimental model PDB 3LF6 4G6F, 3LF6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 295.15 0.1 M PO4-citrate pH 4.2, 40% PEG 600
Crystal Properties Matthews coefficient Solvent content 2.44 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.879 α = 90 b = 66.972 β = 101.46 c = 84.259 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 PIXEL DECTRIS PILATUS 6M 2015-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97950 SSRL BL12-2
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 2.025 36.56 92.1 0.081 7.6 2.5 36193 37
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 2.03 2.07 87 0.535 2.5 1.8
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 4G6F, 3LF6 2.03 36.56 1.34 36187 1810 91.6 0.176 0.174 0.1775 0.213 0.2154 54
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 13.12 f_angle_d 1.007 f_chiral_restr 0.041 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4403 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing