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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 8BS8 experimental model PDB 6QN7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 12.5% w/v PEG 1000,
12.5% w/v PEG 3350,
12.5% v/v MPD,
0.03M Sodium Fluoride,
0.03M Sodium Bromide,
0.03M Sodium Iodide,
0.1 M MOPS/HEPES-Na
Crystal Properties Matthews coefficient Solvent content 2.17 43.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.03 α = 90 b = 70.86 β = 90 c = 96.01 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 2020-02-21 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 1.45 39.74 100 0.07 0.076 0.03 0.999 10.4 6.6 79276
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 1.45 1.47 100 2.604 2.868 1.189 0.325 5.7
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 1.45 39.74 75241 3958 99.96 0.15057 0.14766 0.1476 0.20555 0.2077 RANDOM 24.128
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] 1.53 0.42 -1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.895 r_dihedral_angle_1_deg 7.932 r_rigid_bond_restr 5.463 r_dihedral_angle_2_deg 4.776 r_long_range_B_refined 3.974 r_long_range_B_other 3.973 r_scangle_other 2.955 r_mcangle_it 2.781 r_mcangle_other 2.781 r_scbond_it 2.363
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.895 r_dihedral_angle_1_deg 7.932 r_rigid_bond_restr 5.463 r_dihedral_angle_2_deg 4.776 r_long_range_B_refined 3.974 r_long_range_B_other 3.973 r_scangle_other 2.955 r_mcangle_it 2.781 r_mcangle_other 2.781 r_scbond_it 2.363 r_scbond_other 2.363 r_mcbond_it 2.31 r_mcbond_other 2.31 r_angle_refined_deg 1.639 r_angle_other_deg 0.596 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3507 Nucleic Acid Atoms Solvent Atoms 539 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement pointless data scaling xia2 data reduction PHASER phasing