7Z42 | pdb_00007z42

Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 2B

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	FluPolB PA mutant K135A at 9 mg per ml was mixed with 40 microM of nucleotides 1-13 vRNA 5prime end, 5-pAGUAGUAACAAGA-3, and 1.8 mM 28-mer CTD peptide, YSPTpSPS x 4 in a buffer containing 50 mM HEPES pH 7.5, 500 mM NaCl, 5% glycerol, 2 mM TCEP. Hanging drops for crystallization were set up at 20 C.

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.93	α = 90
b = 202.269	β = 110.538
c = 135.733	γ = 90

Symmetry
Space Group	P 1 21 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		2017-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.25422	ESRF	ID29

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	2.418	127.106	61.4	0.112	0.136	0.992	7.7	3		154519

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	2.42	2.69	64		0.618	0.769	0.63	1.9	2.5

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	5FMZ	2.418	127.106	154519	7573	61.415	0.225	0.2233	0.22	0.2567	0.26	54.204

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]
-0.034		0.054	0.129		-0.105

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.528
r_dihedral_angle_4_deg	17.463
r_dihedral_angle_3_deg	16.749
r_dihedral_angle_1_deg	5.258
r_lrange_it	4.204
r_lrange_other	4.204
r_mcangle_it	2.328
r_mcangle_other	2.328
r_scangle_it	1.888
r_scangle_other	1.888
r_mcbond_it	1.303
r_mcbond_other	1.303
r_angle_refined_deg	1.197
r_angle_other_deg	1.056
r_scbond_it	1.03
r_scbond_other	1.03
r_symmetry_nbd_refined	0.228
r_ext_dist_refined_d	0.218
r_nbd_other	0.176
r_nbd_refined	0.172
r_symmetry_nbd_other	0.163
r_symmetry_xyhbond_nbd_refined	0.158
r_nbtor_refined	0.15
r_xyhbond_nbd_refined	0.138
r_ncsr_local_group_5	0.088
r_ncsr_local_group_3	0.085
r_ncsr_local_group_1	0.074
r_symmetry_nbtor_other	0.072
r_ncsr_local_group_2	0.064
r_chiral_restr	0.046
r_ncsr_local_group_4	0.016
r_bond_refined_d	0.003
r_gen_planes_refined	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	35189
Nucleic Acid Atoms	532
Solvent Atoms	206
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing