Experiment: 9MRW

Functional Implications of Hexameric Dynamics in SARS-CoV-2 Nsp15

X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7K9P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	7.5	298	100 mM HEPES-NaOH, pH 7.5, 200 mM calcium acetate, 8% (w/v) PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
5.11	75.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.2	α = 90
b = 154.2	β = 90
c = 116.2	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	298	PIXEL	PSI JUNGFRAU 4M		2023-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.075	ESRF	ID29

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		fixed target

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Frames Indexed	Latices Merged
1	55068	48079	55068

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	3	30	100	0.98	6.8	420		31487			80.2

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	3	3.11			0.27	1.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	FREE R-VALUE	3	29.64	29954	1544	99.87	0.16867	0.16741	0.1751	0.19318	0.1936	RANDOM	82.248

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]
0.52	0.26		0.52		-1.7

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	13.129
r_long_range_B_other	13.129
r_dihedral_angle_3_deg	12.072
r_scangle_other	10.785
r_mcangle_it	8.02
r_mcangle_other	8.02
r_scbond_it	7.078
r_scbond_other	7.077
r_dihedral_angle_1_deg	5.783
r_mcbond_it	5.353

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	13.129
r_long_range_B_other	13.129
r_dihedral_angle_3_deg	12.072
r_scangle_other	10.785
r_mcangle_it	8.02
r_mcangle_other	8.02
r_scbond_it	7.078
r_scbond_other	7.077
r_dihedral_angle_1_deg	5.783
r_mcbond_it	5.353
r_mcbond_other	5.34
r_angle_refined_deg	0.929
r_angle_other_deg	0.348
r_chiral_restr	0.046
r_bond_refined_d	0.005
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	5492
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
PDB-REDO	refinement
CrystFEL	data reduction
XDS	data scaling
MOLREP	phasing

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.