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Crystal structure of 10E8 Fab 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 7 293.15 0.1 M Hepes pH 7.0, 15% PEG 20,000
Crystal Properties Matthews coefficient Solvent content 2.53 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.1 α = 90 b = 158.97 β = 97.98 c = 99.69 γ = 90
Symmetry Space Group P 1 21 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 CCD MARMOSAIC 300 mm CCD 2013-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03314 APS 23-ID-B
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 2.096 47.142 97.5 0.074 9.3 2.4 72210 34
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 2.1 2.15 91.9 0.63 1.6 2.3
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 2.1 47.14 1.34 72183 3620 97.4 0.18 0.178 0.1802 0.218 0.2198 53
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 12.47 f_angle_d 0.877 f_chiral_restr 0.058 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8879 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms 117
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing