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Bovine naive ultralong antibody AbD08 collected at 100K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K3D experimental model PDB 6QN7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 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
Crystal Properties Matthews coefficient Solvent content 2.12372351 42.1188431
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.5 α = 90 b = 71.11 β = 90 c = 98.41 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 100 PIXEL DECTRIS EIGER X 16M 130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable focus beam 2019-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.59 57.64 99.9 0.058 0.063 0.024 0.999 13.5 6.7 60610
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.62 99.9 1.307 1.416 0.541 0.62 6.8
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 1.59 57.64 57461 3079 99.94 0.17683 0.1745 0.1775 0.21889 0.2179 RANDOM 26.25
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] 0.56 -0.67 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.803 r_dihedral_angle_1_deg 7.87 r_long_range_B_refined 7.111 r_long_range_B_other 6.901 r_dihedral_angle_2_deg 6.109 r_scangle_other 3.629 r_mcangle_it 2.845 r_mcangle_other 2.845 r_scbond_it 2.526 r_scbond_other 2.525
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.803 r_dihedral_angle_1_deg 7.87 r_long_range_B_refined 7.111 r_long_range_B_other 6.901 r_dihedral_angle_2_deg 6.109 r_scangle_other 3.629 r_mcangle_it 2.845 r_mcangle_other 2.845 r_scbond_it 2.526 r_scbond_other 2.525 r_mcbond_it 1.953 r_mcbond_other 1.932 r_angle_refined_deg 1.478 r_angle_other_deg 0.516 r_chiral_restr 0.07 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.001 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 3490 Nucleic Acid Atoms Solvent Atoms 590 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement pointless data scaling xia2 data reduction PHASER phasing