8A2E | pdb_00008a2e

Crystal Structure of Human Parechovirus 3 2A protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7ZTW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1.7 M Ammonium sulphate, 0.05 M Sodium Cacodylate pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.68	α = 90
b = 141.68	β = 90
c = 183.88	γ = 120

Symmetry
Space Group	H 3

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		2014-10-17	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)	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	2.29	102	100	0.11	1	22.86	10.2		61983

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.29	2.34			1.117	0.59

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)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7ZTW	2.29	73.576	61971	3220	99.971	0.18	0.1783	0.18	0.2144	0.21	75.014

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]
3.792			3.792		-7.584

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.019
r_dihedral_angle_4_deg	18.586
r_dihedral_angle_3_deg	15.101
r_lrange_it	8.018
r_lrange_other	8.017
r_dihedral_angle_1_deg	6.875
r_scangle_it	5.299
r_scangle_other	5.262
r_mcangle_it	4.684
r_mcangle_other	4.684
r_scbond_it	3.504
r_scbond_other	3.461
r_mcbond_it	3.163
r_mcbond_other	3.163
r_angle_refined_deg	1.318
r_angle_other_deg	1.226
r_nbd_other	0.247
r_nbd_refined	0.199
r_symmetry_nbd_other	0.179
r_symmetry_xyhbond_nbd_refined	0.168
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.149
r_symmetry_nbd_refined	0.149
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.054
r_symmetry_xyhbond_nbd_other	0.05
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9030
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	70

Software

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