7Z1C

Nanobody H11-B5 and H11-F2 bound to RBD


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6ZBP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2936% v/v Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, 25% w/v Polyethylene glycol 4,000
Crystal Properties
Matthews coefficientSolvent content
3.1661.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.9α = 80.08
b = 56.94β = 87.52
c = 115.89γ = 66.11
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.95296.40.0430.998103.699469
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.950.504

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 REPLACEMENTTHROUGHOUT6ZBP1.95294604491696.430.17610.174910.1994RANDOM62.612
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]
1.88-1.120.050.242.79-1.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.239
r_dihedral_angle_4_deg16.159
r_dihedral_angle_3_deg13.88
r_long_range_B_other7.929
r_long_range_B_refined7.927
r_dihedral_angle_1_deg7.009
r_scangle_other5.346
r_scbond_it3.725
r_scbond_other3.725
r_mcangle_it3.665
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.239
r_dihedral_angle_4_deg16.159
r_dihedral_angle_3_deg13.88
r_long_range_B_other7.929
r_long_range_B_refined7.927
r_dihedral_angle_1_deg7.009
r_scangle_other5.346
r_scbond_it3.725
r_scbond_other3.725
r_mcangle_it3.665
r_mcangle_other3.665
r_mcbond_it2.556
r_mcbond_other2.554
r_angle_refined_deg1.391
r_angle_other_deg1.238
r_chiral_restr0.058
r_bond_refined_d0.007
r_gen_planes_refined0.006
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 Atoms7027
Nucleic Acid Atoms
Solvent Atoms339
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing