7OAU

Nanobody C5 bound to Kent variant RBD (N501Y)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7OAO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M Ammonium fluoride and 20 % Peg 3350
Crystal Properties
Matthews coefficientSolvent content
2.1943.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 28.81α = 90
b = 153.73β = 100.33
c = 75.85γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9999DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.65391000.0441106.677705
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.691000.560.61.26

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7OAO1.6538.46277679377699.9670.1770.17540.199229.12
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]
0.020.707-2.1631.768
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.749
r_dihedral_angle_4_deg16.287
r_dihedral_angle_3_deg11.56
r_dihedral_angle_1_deg6.913
r_lrange_it5.963
r_lrange_other5.961
r_scangle_it3.356
r_scangle_other3.355
r_scbond_it2.179
r_scbond_other2.179
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.749
r_dihedral_angle_4_deg16.287
r_dihedral_angle_3_deg11.56
r_dihedral_angle_1_deg6.913
r_lrange_it5.963
r_lrange_other5.961
r_scangle_it3.356
r_scangle_other3.355
r_scbond_it2.179
r_scbond_other2.179
r_mcangle_it1.893
r_mcangle_other1.892
r_angle_refined_deg1.337
r_angle_other_deg1.323
r_mcbond_it1.314
r_mcbond_other1.314
r_nbd_refined0.18
r_symmetry_nbd_other0.173
r_nbtor_refined0.168
r_symmetry_nbd_refined0.159
r_nbd_other0.159
r_xyhbond_nbd_refined0.152
r_symmetry_xyhbond_nbd_refined0.136
r_symmetry_nbtor_other0.073
r_ncsr_local_group_20.064
r_chiral_restr0.06
r_ncsr_local_group_10.056
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4892
Nucleic Acid Atoms
Solvent Atoms470
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing