7OA4 | pdb_00007oa4

Crystal structure of the N-terminal endonuclease domain of La Crosse virus L-protein bound to compound L-742,001

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XI7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	3.4M Na-formate 0.1M Tris-HCl pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
3.83	67.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.79	α = 90
b = 124.79	β = 90
c = 295.74	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		2020-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.97563	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.9	108.071	100	0.23	0.043	0.994	13.2	27.8		31157			49.67

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	2.9	2.95	99.7		0.202	0.909	2.2	27.09

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	2XI7	2.9	108.071	31073	1542	99.981	0.199	0.197	0.21	0.2386	0.24	52.961

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]
0.393	0.197		0.393		-1.276

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.228
r_dihedral_angle_3_deg	15.762
r_dihedral_angle_4_deg	13.343
r_dihedral_angle_1_deg	5.768
r_lrange_it	5.296
r_lrange_other	5.294
r_scangle_it	2.496
r_scangle_other	2.496
r_mcangle_it	2.237
r_mcangle_other	2.237
r_scbond_it	1.411
r_scbond_other	1.411
r_mcbond_it	1.302
r_mcbond_other	1.302
r_angle_refined_deg	1.211
r_angle_other_deg	1.084
r_symmetry_xyhbond_nbd_refined	0.221
r_nbd_refined	0.183
r_nbtor_refined	0.163
r_symmetry_nbd_other	0.16
r_nbd_other	0.159
r_xyhbond_nbd_refined	0.158
r_symmetry_nbd_refined	0.128
r_symmetry_nbtor_other	0.072
r_symmetry_xyhbond_nbd_other	0.062
r_chiral_restr	0.046
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
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	102
Heterogen Atoms	142

Software

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