7LUX | pdb_00007lux

AALALL segment from the Nucleoprotein of SARS-CoV-2, residues 217-222, crystal form 2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		ideal beta strand AAAAA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9.5	298	polyethylene glycol 3000, CHES, pH 9.5

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.46	α = 90
b = 9.54	β = 90
c = 10.95	γ = 90

Symmetry
Space Group	P 21 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 EIGER X 16M		2020-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9792	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.3	22.23	93	0.105	0.121	0.997	5.94	3.781		1234			20.927

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.36	84.8		0.808	0.922	0.544	1.8	3.957

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	ideal beta strand AAAAA	1.303	22.23	1234	124	92.992	0.199	0.1948	0.2	0.236	0.24	16.319

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]
0.451			-0.87		0.419

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.102
r_dihedral_angle_3_deg	5.506
r_lrange_it	4.505
r_lrange_other	4.406
r_scangle_it	3.021
r_scangle_other	2.99
r_mcangle_other	2.735
r_mcangle_it	2.714
r_scbond_it	1.833
r_scbond_other	1.811
r_mcbond_it	1.649
r_mcbond_other	1.458
r_angle_refined_deg	1.179
r_angle_other_deg	0.869
r_nbd_other	0.154
r_symmetry_nbd_other	0.127
r_symmetry_nbtor_other	0.086
r_nbtor_refined	0.085
r_symmetry_xyhbond_nbd_refined	0.079
r_chiral_restr	0.045
r_xyhbond_nbd_refined	0.017
r_symmetry_nbd_refined	0.008
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	40
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction