8P2T

Bovine naive ultralong antibody AbD08* collected at 100K


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8BS8 
experimental modelPDB 6QN7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529812.5% 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 coefficientSolvent content
2.1743.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.03α = 90
b = 70.86β = 90
c = 96.01γ = 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 beam2020-02-21MSINGLE 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
11.4539.741000.070.0760.030.99910.46.679276
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)
11.451.471002.6042.8681.1890.3255.7

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 REPLACEMENTTHROUGHOUT1.4539.7475241395899.960.150570.147660.20555RANDOM24.128
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]
1.530.42-1.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.895
r_dihedral_angle_1_deg7.932
r_rigid_bond_restr5.463
r_dihedral_angle_2_deg4.776
r_long_range_B_refined3.974
r_long_range_B_other3.973
r_scangle_other2.955
r_mcangle_it2.781
r_mcangle_other2.781
r_scbond_it2.363
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.895
r_dihedral_angle_1_deg7.932
r_rigid_bond_restr5.463
r_dihedral_angle_2_deg4.776
r_long_range_B_refined3.974
r_long_range_B_other3.973
r_scangle_other2.955
r_mcangle_it2.781
r_mcangle_other2.781
r_scbond_it2.363
r_scbond_other2.363
r_mcbond_it2.31
r_mcbond_other2.31
r_angle_refined_deg1.639
r_angle_other_deg0.596
r_chiral_restr0.09
r_bond_refined_d0.011
r_gen_planes_refined0.01
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3507
Nucleic Acid Atoms
Solvent Atoms539
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
pointlessdata scaling
xia2data reduction
PHASERphasing