7IDX | pdb_00007idx

PanDDA analysis group deposition -- SARS-CoV-2 Nsp1 crystal E12 (dataset 1) from the KIT library screening campaign, data used for ground state calculation

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7EQ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1 M HEPES pH 7.5 and 25% (w/v) PEG 3350. Reproducibility was improved by seeding.

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.577	α = 90
b = 36.577	β = 90
c = 141.8	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2023-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.82	36.58	100	0.165	0.173	0.051	0.996	5.8	11.3		9376

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.82	1.85		100	4.216	4.449	1.384	0.18		10.1

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	THROUGHOUT	1.82	35.48	8096	430	91.88	0.23585	0.23341	0.2408	0.2794	0.2359	RANDOM	40.044

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]
-0.31			-0.31		0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.091
r_dihedral_angle_3_deg	14.265
r_dihedral_angle_4_deg	10.023
r_long_range_B_refined	9.505
r_long_range_B_other	9.155
r_dihedral_angle_1_deg	7.841
r_scangle_other	5.999
r_mcangle_other	4.805
r_mcangle_it	4.8
r_scbond_it	3.733
r_scbond_other	3.731
r_mcbond_it	3.335
r_mcbond_other	3.323
r_angle_refined_deg	1.56
r_angle_other_deg	1.204
r_chiral_restr	0.062
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	873
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PHASER	phasing
DIALS	data scaling
DIALS	data reduction