6TSD | pdb_00006tsd

Crystal structure of human coxsackievirus A24v in complex with pentavalent inhibitor ME0752

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4Q4W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	200 mM Magnesium chloride, 3.4 M 1,6-Hexanediol, 100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 305.475	α = 90
b = 365.351	β = 90
c = 366.484	γ = 90

Symmetry
Space Group	I 2 2 2

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		2016-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.81	50	99.9	0.993	8.18	7.71		14074225

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	1.81	1.92	99.4		0.679

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	4Q4w	1.81	49.955	1824194		99.892	0.15	0.1502	0.41		29.473

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]
0.084			-0.174		0.091

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.347
r_dihedral_angle_4_deg	15.944
r_dihedral_angle_3_deg	11.624
r_dihedral_angle_1_deg	9.128
r_lrange_it	7.029
r_lrange_other	6.835
r_scangle_it	5.436
r_scangle_other	5.435
r_scbond_other	4.011
r_scbond_it	3.995
r_mcangle_other	2.59
r_mcangle_it	2.588
r_mcbond_it	1.962
r_mcbond_other	1.96
r_angle_refined_deg	1.381
r_angle_other_deg	1.282
r_xyhbond_nbd_other	0.76
r_symmetry_nbd_refined	0.757
r_nbd_other	0.692
r_nbd_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.162
r_symmetry_nbd_other	0.161
r_xyhbond_nbd_refined	0.117
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.065
r_metal_ion_refined	0.029
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6519
Nucleic Acid Atoms
Solvent Atoms	816
Heterogen Atoms	67

Software

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