6QKD

CRYSTAL STRUCTURE OF vhh-based FAB-fragment of antibody BCD-085


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529850 mM Na-Ac pH 5.5, 150 mM NaCl with 1.5 M (NH4)2SO4, 150 mM sodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.2144.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.56α = 90
b = 111.92β = 90
c = 165.43γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2018-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97242ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.95099.90.05319.26.2132510
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.95

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT5I1K, 5FGB1.947.6125855662499.70.171730.168720.22802RANDOM48.813
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]
0.45-0.650.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.042
r_sphericity_free32.781
r_sphericity_bonded21.487
r_dihedral_angle_4_deg20.309
r_dihedral_angle_3_deg14.823
r_long_range_B_refined9.198
r_long_range_B_other9.169
r_scangle_other8.055
r_mcangle_it7.787
r_mcangle_other7.787
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.042
r_sphericity_free32.781
r_sphericity_bonded21.487
r_dihedral_angle_4_deg20.309
r_dihedral_angle_3_deg14.823
r_long_range_B_refined9.198
r_long_range_B_other9.169
r_scangle_other8.055
r_mcangle_it7.787
r_mcangle_other7.787
r_scbond_it6.794
r_rigid_bond_restr6.738
r_scbond_other6.607
r_mcbond_it6.428
r_mcbond_other6.426
r_dihedral_angle_1_deg6.418
r_angle_refined_deg1.291
r_angle_other_deg1.186
r_chiral_restr0.07
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13122
Nucleic Acid Atoms
Solvent Atoms316
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing