7LTU | pdb_00007ltu

AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2, RESIDUES 217-222, CRYSTAL FORM 1

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, AAAAAA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	4	298	trifluoroacetic acid

Crystal Properties
Matthews coefficient	Solvent content
1.69	27.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 9.45	α = 74.88
b = 11.34	β = 79.13
c = 20.27	γ = 67.77

Symmetry
Space Group	P 1

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	1.12	19.47	78.4	0.084	0.107	0.985	5.92	2.366		2270			14.896

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	1.12	1.18	31.1		0.397	0.511	0.892	2.02	2.375

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, AAAAAA	1.122	19.469	2269	227	79.114	0.159	0.1548	0.16	0.1953	0.21	12.753

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]
-0.438	-0.528	-0.809	0.262	1.611	0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.602
r_dihedral_angle_1_deg	5.953
r_scangle_it	4.99
r_scbond_it	3.925
r_lrange_it	2.941
r_lrange_other	2.572
r_scangle_other	2.385
r_mcangle_other	1.978
r_mcangle_it	1.955
r_mcbond_it	1.731
r_scbond_other	1.695
r_mcbond_other	1.671
r_angle_other_deg	1.311
r_angle_refined_deg	1.306
r_rigid_bond_restr	0.872
r_nbd_other	0.208
r_symmetry_nbd_refined	0.206
r_symmetry_nbd_other	0.172
r_nbd_refined	0.136
r_nbtor_refined	0.131
r_symmetry_nbtor_other	0.105
r_symmetry_xyhbond_nbd_refined	0.09
r_chiral_restr	0.068
r_xyhbond_nbd_refined	0.068
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	80
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	21

Software

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