13ZN | pdb_000013zn

PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3Dpol in complex with Z432057220

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
2.5	50.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.555	α = 90
b = 84.612	β = 108.15
c = 59.227	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	1.76	56.26	99.9	0.139	0.151	0.058	0.996	7.5	6.6		51503

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	1.76	1.8	97.8		2.948	3.299	1.452	0.433		4.9

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	1.76	56.28	46492	2485	94.96	0.242	0.2393	0.2643	0.2917	0.311	RANDOM	45.473

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]
-4.39		-0.02	5.97		-1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.263
r_dihedral_angle_3_deg	15.247
r_dihedral_angle_4_deg	15.058
r_dihedral_angle_1_deg	7.298
r_mcangle_it	4.827
r_mcbond_it	3.459
r_mcbond_other	3.45
r_angle_refined_deg	1.489
r_angle_other_deg	1.212
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
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	323
Heterogen Atoms	84

Software

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