7OAQ

Nanobody H3 AND C1 bound to RBD with Kent mutation


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2931.0 M Lithium chloride, 0.1 M Citrate pH 4, 20 % Peg 6000
Crystal Properties
Matthews coefficientSolvent content
2.9558.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.857α = 90
b = 105.857β = 90
c = 112.709γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9762DiamondI04

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
11.55531000.02116.926.893033
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)
11.551.59930.590.60.627.6

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-VALUE7oap1.5552.98492354472299.270.1560.1550.178336.162
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]
-1.211-1.2112.422
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.114
r_dihedral_angle_4_deg14.157
r_dihedral_angle_3_deg12.225
r_rigid_bond_restr8.608
r_dihedral_angle_1_deg6.728
r_lrange_other3.96
r_lrange_it3.954
r_scangle_it3.642
r_scangle_other3.642
r_scbond_it3.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.114
r_dihedral_angle_4_deg14.157
r_dihedral_angle_3_deg12.225
r_rigid_bond_restr8.608
r_dihedral_angle_1_deg6.728
r_lrange_other3.96
r_lrange_it3.954
r_scangle_it3.642
r_scangle_other3.642
r_scbond_it3.102
r_scbond_other3.022
r_mcangle_other2.776
r_mcangle_it2.774
r_mcbond_it2.317
r_mcbond_other2.276
r_angle_refined_deg1.398
r_angle_other_deg1.34
r_symmetry_nbd_refined0.222
r_nbd_refined0.21
r_symmetry_nbd_other0.183
r_xyhbond_nbd_refined0.174
r_nbtor_refined0.173
r_symmetry_xyhbond_nbd_refined0.147
r_nbd_other0.142
r_symmetry_nbtor_other0.076
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3513
Nucleic Acid Atoms
Solvent Atoms375
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing