7NKT

RBD domain of SARS-CoV2 in complex with neutralizing nanobody NM1226


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Z1Z6Z1Z, 6XC4
experimental modelPDB 6XC46Z1Z, 6XC4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP527750mM K2HPO4, 20% (w/v) PEG 8000
Crystal Properties
Matthews coefficientSolvent content
3.867.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.093α = 90
b = 128.093β = 90
c = 77.676γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2020-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.9999SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.29746.10399.90.99919.59.128115
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)
12.2972.4499.60.4841.4

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-VALUE6Z1Z, 6XC42.346.10328115168799.9080.1870.18430.223959.942
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]
0.6820.682-1.364
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.612
r_dihedral_angle_4_deg19.526
r_dihedral_angle_3_deg15.138
r_lrange_other8.578
r_lrange_it8.57
r_dihedral_angle_1_deg7.715
r_scangle_it5.482
r_scangle_other5.426
r_mcangle_other5.264
r_mcangle_it5.262
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.612
r_dihedral_angle_4_deg19.526
r_dihedral_angle_3_deg15.138
r_lrange_other8.578
r_lrange_it8.57
r_dihedral_angle_1_deg7.715
r_scangle_it5.482
r_scangle_other5.426
r_mcangle_other5.264
r_mcangle_it5.262
r_scbond_it3.99
r_scbond_other3.87
r_mcbond_it3.653
r_mcbond_other3.64
r_angle_refined_deg1.463
r_angle_other_deg1.262
r_symmetry_nbd_refined0.223
r_nbd_other0.207
r_nbd_refined0.19
r_symmetry_nbd_other0.179
r_nbtor_refined0.176
r_xyhbond_nbd_refined0.142
r_symmetry_xyhbond_nbd_refined0.142
r_symmetry_nbtor_other0.077
r_chiral_restr0.066
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 Atoms2503
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing