8CNX | pdb_00008cnx

Structure of Enterovirus D68 3C protease

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZV8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.14	293	25% PEG 3,350 0.1 M Tris 0.2 M Ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.82	α = 90
b = 62.53	β = 90
c = 147.36	γ = 90

Symmetry
Space Group	P 21 21 21

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 X 9M		2023-01-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9212	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.49	38.63	91.9	0.099	0.998	11.4	10.5		60463

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.49	1.53	56.7		0.388	0.7	4.1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.49	38.627	60384	3016	92.043	0.204	0.2036	0.21	0.2199	0.23	25.167

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]
-1.2			2.642		-1.441

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.856
r_dihedral_angle_3_deg	14.637
r_dihedral_angle_1_deg	7.312
r_lrange_it	6.526
r_lrange_other	6.511
r_dihedral_angle_2_deg	6.348
r_scangle_it	5.24
r_scangle_other	5.238
r_mcangle_other	3.525
r_mcangle_it	3.523
r_scbond_it	3.518
r_scbond_other	3.517
r_mcbond_it	2.666
r_mcbond_other	2.642
r_angle_refined_deg	1.581
r_angle_other_deg	0.902
r_symmetry_xyhbond_nbd_refined	0.321
r_symmetry_nbd_refined	0.282
r_nbd_refined	0.225
r_symmetry_nbd_other	0.201
r_nbd_other	0.196
r_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.173
r_xyhbond_nbd_other	0.143
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.08
r_bond_other_d	0.036
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2808
Nucleic Acid Atoms
Solvent Atoms	313
Heterogen Atoms

Software

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