8CIF

Bovine naive ultralong antibody AbD08 collected at 293K


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8BS8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.1M 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
2VAPOR DIFFUSION, SITTING DROP8.52930.1M 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
3VAPOR DIFFUSION, SITTING DROP8.52930.1M 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
4VAPOR DIFFUSION, SITTING DROP8.52930.1M 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 coefficientSolvent content
1.9938.29
1.9938.29
1.9938.29
1.9938.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.228α = 90
b = 71.585β = 90
c = 100.233γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS EIGER2 X 4M130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable microfocus beam2019-12-02MSINGLE WAVELENGTH
22x-ray293PIXELDECTRIS EIGER2 X 4M130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable microfocus beam2019-12-02MSINGLE WAVELENGTH
33x-ray293PIXELDECTRIS EIGER2 X 4M130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable microfocus beam2019-12-02MSINGLE WAVELENGTH
44x-ray293PIXELDECTRIS EIGER2 X 4M130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable microfocus beam2019-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE VMXi0.9795DiamondVMXi
2SYNCHROTRONDIAMOND BEAMLINE VMXi0.9795DiamondVMXi
3SYNCHROTRONDIAMOND BEAMLINE VMXi0.9795DiamondVMXi
4SYNCHROTRONDIAMOND BEAMLINE VMXi0.9795DiamondVMXi

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
22.0758.27760.103161.921940
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)RedundancyNumber Unique Reflections (All)
22.072.110.8310.50.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.258.3221885112795.450.179630.177130.22786RANDOM36.51
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]
-0.070.020.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.732
r_dihedral_angle_4_deg14.589
r_dihedral_angle_3_deg13.898
r_dihedral_angle_1_deg8.295
r_long_range_B_refined7.671
r_long_range_B_other7.665
r_scangle_other5.46
r_mcangle_it4.691
r_mcangle_other4.69
r_scbond_it3.564
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.732
r_dihedral_angle_4_deg14.589
r_dihedral_angle_3_deg13.898
r_dihedral_angle_1_deg8.295
r_long_range_B_refined7.671
r_long_range_B_other7.665
r_scangle_other5.46
r_mcangle_it4.691
r_mcangle_other4.69
r_scbond_it3.564
r_scbond_other3.555
r_mcbond_it3.059
r_mcbond_other3.047
r_angle_refined_deg1.522
r_angle_other_deg1.3
r_chiral_restr0.065
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms3415
Nucleic Acid Atoms
Solvent Atoms52
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata scaling
DIALSdata reduction
PHASERphasing