7K9P

Room temperature structure of NSP15 Endoribonuclease from SARS CoV-2 solved using SFX.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE5.5295NendoU protein 75 mg/ml (20 mM HEPES pH 7.5, 150mM NaCl, 1mM TCEP) is added to the precipitant solution (100mM Na Citrate pH 5.5, 20% PEG 1000, 20% 2-Methyl-2,4-pentanediol (MPD)) in a 1:7 protein:precipitant ratio with agitation at 295K overnight.
Crystal Properties
Matthews coefficientSolvent content
5.1175.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154α = 90
b = 154β = 90
c = 117γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295PIXELSLAC ePix10k 2M2020-09-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.277SLAC LCLSMFX

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1injection
Injection
Diffraction IDDescriptionFlow RateInjector DiameterInjection PowerInjector NozzleFilter SizeCarrier Solvent
1MESH injector
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
130120
Data Reduction
Diffraction IDFrames IndexedCrystal HitsTotal Frames
125066

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
12.633.671000.943.110148524
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)
12.62.691000.030.270

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6xdh2.633.6745981250399.90.192290.191370.20877RANDOM47.684
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]
-8.54-8.5417.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.26
r_dihedral_angle_3_deg14.785
r_dihedral_angle_4_deg13.657
r_dihedral_angle_1_deg5.347
r_long_range_B_refined1.278
r_long_range_B_other1.278
r_angle_refined_deg1.034
r_angle_other_deg0.909
r_mcangle_it0.829
r_mcangle_other0.829
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.26
r_dihedral_angle_3_deg14.785
r_dihedral_angle_4_deg13.657
r_dihedral_angle_1_deg5.347
r_long_range_B_refined1.278
r_long_range_B_other1.278
r_angle_refined_deg1.034
r_angle_other_deg0.909
r_mcangle_it0.829
r_mcangle_other0.829
r_scangle_other0.502
r_mcbond_it0.458
r_mcbond_other0.458
r_scbond_it0.267
r_scbond_other0.266
r_chiral_restr0.06
r_bond_refined_d0.006
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 Atoms5504
Nucleic Acid Atoms
Solvent Atoms16
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
Aimlessdata scaling
MOLREPphasing