13YH | pdb_000013yh

PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3Dpol in complex with Z169675004

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5XE0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	0.1 M TRIS-HCl (pH 8.5), 16% PEG 3350, 16% Isopropanol

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.336	α = 90
b = 83.102	β = 108.53
c = 58.769	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 EIGER2 XE 9M		2024-11-15		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92202	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.67	83.12	99.8	0.142	0.155	0.061	0.99	19	6.3		58356

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.67	1.7	95.3		1.806	2.061	0.977	0.424		4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1.67	55.72	55227	2960	99.61	0.1833	0.1816	0.1928	0.2153	0.2177	RANDOM	22.945

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]
-0.74		0.65	0.64		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.81
r_dihedral_angle_4_deg	17.259
r_dihedral_angle_3_deg	13.436
r_dihedral_angle_1_deg	6.764
r_mcangle_it	2.788
r_mcbond_it	1.974
r_mcbond_other	1.958
r_angle_refined_deg	1.667
r_angle_other_deg	1.414
r_chiral_restr	0.088
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3639
Nucleic Acid Atoms
Solvent Atoms	328
Heterogen Atoms	104

Software

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