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Crystal structure of 10E8 Fab in complex with the MPER epitope scaffold T117v2 and phosphatidylglycerol (06:0 PG)
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 7 293.15 50% PEG 200, 0.1 M Hepes pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.78 55.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.006 α = 90 b = 67.287 β = 90 c = 194.678 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 110 PIXEL DECTRIS PILATUS 6M 2014-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97945 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.373 48.669 95.7 0.086 0.915 8.5 3.5 28788 62
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.373 2.4 98.1 0.702 0.627 1.8 3.7
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 2.373 48.669 1.34 28737 1437 95.39 0.1979 0.1952 0.2035 0.2504 0.2577 70
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 14.032 f_angle_d 1.107 f_chiral_restr 0.044 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4541 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing