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Structure of NHP D11A.F2 Fab in complex with 16055 V2b peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RFO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.1 M Tris pH 8.0 and 1.32 M K/Na Tartrate at 8.5 mg/ml.
Cryo protection: 15% 2R3R Butanediol
Crystal Properties Matthews coefficient Solvent content 4.27 71.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.393 α = 90 b = 130.393 β = 90 c = 170.898 γ = 120
Symmetry Space Group P 61 2 2
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 PILATUS3 6M 2017-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.9774 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.8 94.22 99.8 0.083 0.72 11.9 22.2 21787 52.57
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 2.8 2.95 98.9 0.744 22.2
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4RFO 2.8 94.21 1.34 21700 1092 99.66 0.2183 0.2163 0.2548 0.2259 57.93
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 17.4396 f_angle_d 0.9583 f_chiral_restr 0.0523 f_bond_d 0.0098 f_plane_restr 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3428 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 82
Software Software Software Name Purpose PHENIX refinement Coot model building SCALEPACK data scaling PHASER phasing HKL-2000 data reduction