7B27

RBD domain SARS-CoV2 in complex with neutralizing nanobody NM1230


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6XC46XC4, 6Z1Z
experimental modelPDB 6Z1Z6XC4, 6Z1Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.9293200 mM MgCl2, 20% (w/v) PEG 3350, pH 5.9
Crystal Properties
Matthews coefficientSolvent content
2.5551.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.29α = 90
b = 63.29β = 90
c = 411.91γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90PIXELDECTRIS EIGER X 16M2020-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.999998SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
12.946.593.50.2070.9987.86.061849361
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.92.9895.71.860.6621.15

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-VALUE6XC4, 6Z1Z2.90230.00218475129393.440.2690.26610.305167.189
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]
4.2564.256-8.511
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.602
r_dihedral_angle_3_deg19.805
r_dihedral_angle_4_deg17.164
r_lrange_it6.835
r_lrange_other6.832
r_mcangle_it4.561
r_mcangle_other4.56
r_dihedral_angle_1_deg4.015
r_scangle_it3.86
r_scangle_other3.859
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.602
r_dihedral_angle_3_deg19.805
r_dihedral_angle_4_deg17.164
r_lrange_it6.835
r_lrange_other6.832
r_mcangle_it4.561
r_mcangle_other4.56
r_dihedral_angle_1_deg4.015
r_scangle_it3.86
r_scangle_other3.859
r_mcbond_it2.695
r_mcbond_other2.691
r_scbond_it2.232
r_scbond_other2.231
r_angle_refined_deg1.217
r_angle_other_deg1.047
r_symmetry_xyhbond_nbd_other0.286
r_symmetry_nbd_refined0.236
r_xyhbond_nbd_refined0.205
r_symmetry_nbd_other0.173
r_nbtor_refined0.164
r_nbd_refined0.162
r_nbd_other0.159
r_symmetry_nbtor_other0.071
r_symmetry_xyhbond_nbd_refined0.054
r_chiral_restr0.031
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4831
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing