8BS8

Bovine naive ultralong antibody AbD08 collected at 100K


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4K3D 
experimental modelPDB 6QN7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52980.1M 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 coefficientSolvent content
2.1237235142.1188431

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.5α = 90
b = 71.11β = 90
c = 98.41γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable focus beam2019-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.5957.6499.90.0580.0630.0240.99913.56.760610
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)RedundancyNumber Unique Reflections (All)
11.591.6299.91.3071.4160.5410.626.8

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 REPLACEMENTTHROUGHOUT1.5957.6457461307999.940.176830.17450.21889RANDOM26.25
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]
0.56-0.670.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.803
r_dihedral_angle_1_deg7.87
r_long_range_B_refined7.111
r_long_range_B_other6.901
r_dihedral_angle_2_deg6.109
r_scangle_other3.629
r_mcangle_it2.845
r_mcangle_other2.845
r_scbond_it2.526
r_scbond_other2.525
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.803
r_dihedral_angle_1_deg7.87
r_long_range_B_refined7.111
r_long_range_B_other6.901
r_dihedral_angle_2_deg6.109
r_scangle_other3.629
r_mcangle_it2.845
r_mcangle_other2.845
r_scbond_it2.526
r_scbond_other2.525
r_mcbond_it1.953
r_mcbond_other1.932
r_angle_refined_deg1.478
r_angle_other_deg0.516
r_chiral_restr0.07
r_gen_planes_refined0.009
r_bond_refined_d0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms3490
Nucleic Acid Atoms
Solvent Atoms590
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
pointlessdata scaling
xia2data reduction
PHASERphasing