7K9P | pdb_00007k9p

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

X-RAY DIFFRACTION

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Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6XDH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	5.5	295	NendoU 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 coefficient	Solvent content
5.11	75.93

Crystal Data

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

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	295	PIXEL	SLAC ePix10k 2M		2020-09-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE MFX	1.277	SLAC LCLS	MFX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		injection

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	30 (fs)	120		undefined (KeV)

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Frames Indexed	Latices Merged
1		25066

Injection
Diffraction ID	Description	Flow Rate	Injector Diameter	Injection Power	Injector Nozzle	Filter Size	Carrier Solvent
1	MESH injector	undefined (µl/min)	undefined (µm)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.6	33.67	100	0.94	3.1	101		48524

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.69	100		0.03	0.2	70

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6xdh	2.6	33.67	45981	2503	99.9	0.19229	0.19137	0.201	0.20877	0.2176	RANDOM	47.684

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			-8.54		17.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.26
r_dihedral_angle_3_deg	14.785
r_dihedral_angle_4_deg	13.657
r_dihedral_angle_1_deg	5.347
r_long_range_B_refined	1.278
r_long_range_B_other	1.278
r_angle_refined_deg	1.034
r_angle_other_deg	0.909
r_mcangle_it	0.829
r_mcangle_other	0.829
r_scangle_other	0.502
r_mcbond_it	0.458
r_mcbond_other	0.458
r_scbond_it	0.267
r_scbond_other	0.266
r_chiral_restr	0.06
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5504
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
Aimless	data scaling
MOLREP	phasing