6ZBP

H11-H4 complex with SARS-CoV-2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YZ5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Crystals were grown at using the sitting drop vapor diffusion method by mixing 0.2 uL of the 18 mg/mL H11-H4 RBD complex with 0.1 uL of the crystallization buffer containing 0.2 M Sodium acetate trihydrate, 0.1 M MES pH 6.0, 20 % w/v PEG 8000. The crystals grew overnight and were flash cooled in a solution containing the mother liquor with 30 % (v/v) ethylene glycol.
Crystal Properties
Matthews coefficientSolvent content
2.6253.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.15α = 90
b = 73.15β = 90
c = 131.67γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2020-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97623DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.8557.15199.50.0860.028118.219.735506
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.999.52.050.460.71.720.9

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6YZ51.8557.15135472180899.7330.1870.1850.190.21690.2248.736
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]
2.0911.0462.091-6.784
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.74
r_dihedral_angle_other_3_deg24.12
r_dihedral_angle_1_deg17.387
r_dihedral_angle_4_deg16.664
r_dihedral_angle_3_deg12.462
r_lrange_other8.808
r_lrange_it8.797
r_scangle_it6.874
r_scangle_other6.777
r_scbond_it4.612
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2546
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata reduction
Aimlessdata scaling
PHASERphasing