6Z6B | pdb_00006z6b

Structure of full-length La Crosse virus L protein (polymerase)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5AMR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	LACV-L in complex with pre-annealed 3 prime (1-16) and 5 prime (9-16) vRNA was concentrated to 5 mg/ml. The 5 prime (1-10) vRNA end was later soaked into crystals in 1 to 2 molar ratio. Mother liquor was 100 mM Tris pH 8.0, 100 mM NaCl, and 8% PEG 4000. Crystals were soaked in a stepwise manner with increasing concentration of the glycerol cryo-protectant, reaching 30%

Crystal Properties
Matthews coefficient	Solvent content
5.42	77.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 371.187	α = 90
b = 145.32	β = 116.333
c = 234.193	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS 6M-F		2014-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9724	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.96	209.891	60.8	0.163	0.995	6.5	11.6		59211

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.96	4.35			1.285	0.47

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	5AMR	3.961	209.891	59211	1514	60.786	0.265	0.2638	0.26	0.2988	0.29	189.756

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]
2.243		-1.674	1.232		-1.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.954
r_dihedral_angle_3_deg	17.299
r_lrange_it	17.253
r_lrange_other	17.253
r_dihedral_angle_4_deg	11.115
r_mcangle_it	11.064
r_mcangle_other	11.064
r_scangle_it	8.98
r_scangle_other	8.98
r_mcbond_it	6.307
r_mcbond_other	6.304
r_dihedral_angle_1_deg	5.017
r_scbond_it	4.781
r_scbond_other	4.781
r_angle_refined_deg	1.156
r_angle_other_deg	1.041
r_symmetry_xyhbond_nbd_refined	0.348
r_ext_dist_refined_d	0.222
r_nbd_other	0.182
r_symmetry_nbd_other	0.172
r_nbd_refined	0.17
r_nbtor_refined	0.159
r_xyhbond_nbd_refined	0.15
r_symmetry_nbd_refined	0.135
r_symmetry_nbtor_other	0.074
r_symmetry_xyhbond_nbd_other	0.066
r_ncsr_local_group_2	0.039
r_chiral_restr	0.038
r_ncsr_local_group_1	0.005
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	33204
Nucleic Acid Atoms	1434
Solvent Atoms
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
MOLREP	phasing