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Crystal structure of EEEV-179 Fab (Crystal Kappa)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.3 M sodium fluoride, 15% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.88 57.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.859 α = 90 b = 73.106 β = 95.31 c = 95.887 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 PIXEL DECTRIS EIGER X 9M 2022-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.25 50 97.2 0.982 11.6 3.5 25428
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 2.25 2.29 91.6 0.837 2.5 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.25 48.24 24115 1313 96.87 0.19068 0.18781 0.195 0.24471 0.2464 RANDOM 48.075
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] 3.47 2.95 -2.94 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.84 r_dihedral_angle_2_deg 10.873 r_long_range_B_other 9.71 r_long_range_B_refined 9.677 r_dihedral_angle_1_deg 8.392 r_scangle_other 7.407 r_mcangle_it 6.864 r_mcangle_other 6.864 r_scbond_it 5.354 r_scbond_other 5.352
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.84 r_dihedral_angle_2_deg 10.873 r_long_range_B_other 9.71 r_long_range_B_refined 9.677 r_dihedral_angle_1_deg 8.392 r_scangle_other 7.407 r_mcangle_it 6.864 r_mcangle_other 6.864 r_scbond_it 5.354 r_scbond_other 5.352 r_mcbond_it 5.066 r_mcbond_other 5.066 r_angle_refined_deg 1.574 r_angle_other_deg 0.559 r_chiral_restr 0.069 r_bond_other_d 0.009 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3319 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing