7PLR | pdb_00007plr

Crystal structure of the N-terminal endonuclease domain of La Crosse virus L-protein bound to compound Baloxavir

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7OA4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	3.4M Sodium Formate 0.1M Tris - HCl pH8.0

Crystal Properties
Matthews coefficient	Solvent content
3.82	67.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.738	α = 90
b = 124.738	β = 90
c = 295.25	γ = 120

Symmetry
Space Group	P 61 2 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		2020-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97856	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.64	108.03	100	0.025	0.999	20.1	39.8		40890

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.64	2.69	100		0.19	0.912	2.2	39.1

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	7OA4	2.64	108.026	40799	2041	100	0.216	0.2136	0.22	0.2539	0.25	55.557

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]
0.811	0.406		0.811		-2.632

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.307
r_dihedral_angle_3_deg	14.438
r_dihedral_angle_4_deg	12.758
r_dihedral_angle_1_deg	5.503
r_lrange_it	4.608
r_lrange_other	4.598
r_scangle_it	2.853
r_scangle_other	2.853
r_mcangle_it	2.687
r_mcangle_other	2.686
r_scbond_it	1.72
r_scbond_other	1.718
r_mcbond_it	1.648
r_mcbond_other	1.648
r_angle_refined_deg	1.204
r_angle_other_deg	1.089
r_symmetry_xyhbond_nbd_refined	0.275
r_nbd_refined	0.185
r_nbtor_refined	0.162
r_symmetry_nbd_other	0.158
r_xyhbond_nbd_refined	0.145
r_symmetry_nbd_refined	0.138
r_nbd_other	0.126
r_symmetry_nbtor_other	0.07
r_xyhbond_nbd_other	0.056
r_chiral_restr	0.045
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6132
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	130

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing