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Crystal structure of glVRC01 Fab in complex with anti-idiotype iv1 scFv
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MFT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M Hepes pH 7.0, PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.21 44.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.019 α = 90 b = 85.244 β = 99.733 c = 113.636 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 100 CCD MARMOSAIC 325 mm CCD 2017-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.2 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.99 50 99.15 0.911 4 1.7 44594 34.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.07 0.822
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 6MFT 1.99 42.62 1.36 44580 2272 99.13 0.182 0.1791 0.1804 0.2354 0.236 41.67
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 11.2794 f_angle_d 0.5059 f_chiral_restr 0.0429 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5074 Nucleic Acid Atoms Solvent Atoms 482 Heterogen Atoms 82
Software Software Software Name Purpose PHASER phasing PHENIX refinement Coot model building Blu-Ice data collection HKL-2000 data scaling