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Bovine naive ultralong antibody AbD08 collected at 293K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BS8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1M Tris (base)
0.1M Bicine
12% (v/v) PEG 500 MME
6% (v/v) PEG 20000
0.15M Sodium chloride
0.09M Sodium fluoride
0.09M Sodium iodide
0.09M Sodium bromide 2 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1M Tris (base)
0.1M Bicine
12% (v/v) PEG 500 MME
6% (v/v) PEG 20000
0.15M Sodium chloride
0.09M Sodium nitrate
0.09M Sodium phosphate dibasic
0.09M Ammonium sulphate 3 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1M Tris (base)
0.1M Bicine
12% (v/v) PEG 500 MME
6% (v/v) PEG 20000
0.15M Sodium chloride
0.09M Sodium nitrate
0.09M Sodium phosphate dibasic
0.09M Ammonium sulphate 4 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1M Tris (base)
0.1M Bicine
12% (v/v) PEG 500 MME
6% (v/v) PEG 20000
0.15M Sodium chloride
0.1M Sodium formate
0.1M Ammonium Acetate
0.1M Sodium citrate tribasic dihydrate
0.1M Potassium sodium tartrate tetrahydrate
0.1M Sodium oxamate
Crystal Properties Matthews coefficient Solvent content 1.99 38.29 1.99 38.29 1.99 38.29 1.99 38.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.228 α = 90 b = 71.585 β = 90 c = 100.233 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 293 PIXEL DECTRIS EIGER2 X 4M 130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable microfocus beam 2019-12-02 M SINGLE WAVELENGTH 2 2 x-ray 293 PIXEL DECTRIS EIGER2 X 4M 130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable microfocus beam 2019-12-02 M SINGLE WAVELENGTH 3 3 x-ray 293 PIXEL DECTRIS EIGER2 X 4M 130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable microfocus beam 2019-12-02 M SINGLE WAVELENGTH 4 4 x-ray 293 PIXEL DECTRIS EIGER2 X 4M 130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable microfocus beam 2019-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE VMXi 0.9795 Diamond VMXi 2 SYNCHROTRON DIAMOND BEAMLINE VMXi 0.9795 Diamond VMXi 3 SYNCHROTRON DIAMOND BEAMLINE VMXi 0.9795 Diamond VMXi 4 SYNCHROTRON DIAMOND BEAMLINE VMXi 0.9795 Diamond VMXi
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 2 2.07 58.27 76 0.103 1 6 1.9 21940
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) 2 2.07 2.11 0.831 0.5 0.5
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 2.2 58.32 21885 1127 95.45 0.17963 0.17713 0.1841 0.22786 0.236 RANDOM 36.51
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] -0.07 0.02 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.732 r_dihedral_angle_4_deg 14.589 r_dihedral_angle_3_deg 13.898 r_dihedral_angle_1_deg 8.295 r_long_range_B_refined 7.671 r_long_range_B_other 7.665 r_scangle_other 5.46 r_mcangle_it 4.691 r_mcangle_other 4.69 r_scbond_it 3.564
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.732 r_dihedral_angle_4_deg 14.589 r_dihedral_angle_3_deg 13.898 r_dihedral_angle_1_deg 8.295 r_long_range_B_refined 7.671 r_long_range_B_other 7.665 r_scangle_other 5.46 r_mcangle_it 4.691 r_mcangle_other 4.69 r_scbond_it 3.564 r_scbond_other 3.555 r_mcbond_it 3.059 r_mcbond_other 3.047 r_angle_refined_deg 1.522 r_angle_other_deg 1.3 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 3415 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data scaling DIALS data reduction PHASER phasing