7OJ7 | pdb_00007oj7

Crystal structure of human coxsackievirus A24v in complex with a pentavalent N-acetylneuraminic acid conjugate

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 = 305.52	α = 90
b = 365.55	β = 90
c = 366.48	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		2018-04-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976250	Diamond	I03

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	1.78	49.962	99.9	0.263	0.282	0.989	6.6	7.7		1921680			22

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	1.78	1.89	99.7		1.331	1.428	0.506	1.1

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	1.78	49.96	1921680		99.919	0.158	0.1577	0.41		32.077

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]
-0.059			0.19		-0.131

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.664
r_dihedral_angle_4_deg	16.065
r_dihedral_angle_3_deg	11.772
r_dihedral_angle_1_deg	9.06
r_lrange_it	7.183
r_lrange_other	6.88
r_scangle_other	5.812
r_scangle_it	5.809
r_scbond_it	4.127
r_scbond_other	4.115
r_mcangle_other	3.001
r_mcangle_it	2.998
r_mcbond_it	2.252
r_mcbond_other	2.24
r_angle_refined_deg	1.371
r_angle_other_deg	1.296
r_symmetry_nbd_refined	0.562
r_nbd_other	0.54
r_nbd_refined	0.184
r_nbtor_refined	0.163
r_symmetry_nbd_other	0.162
r_symmetry_xyhbond_nbd_refined	0.158
r_xyhbond_nbd_refined	0.127
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.064
r_symmetry_xyhbond_nbd_other	0.043
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6529
Nucleic Acid Atoms
Solvent Atoms	816
Heterogen Atoms	34

Software

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