8A2F | pdb_00008a2f

Crystal Structure of Ljunganvirus 1 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	20% PEG3350, 0.2 M sodium formate

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.79	α = 90
b = 58.48	β = 90
c = 110.24	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 PILATUS 6M		2014-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9796	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.73	50	100	0.056	23.8	12.7		27964

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.73	1.77			1.26	1.9	11.3

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	1.73	50	27588	1448	99.92	0.182	0.1803	0.19	0.2145	0.22	37.949

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]
0.96			-1.219		0.259

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.818
r_dihedral_angle_3_deg	13.554
r_dihedral_angle_2_deg	11.613
r_lrange_other	9.214
r_lrange_it	9.206
r_dihedral_angle_1_deg	6.909
r_scangle_it	6.72
r_scangle_other	6.718
r_mcangle_it	5.086
r_mcangle_other	5.086
r_scbond_it	4.974
r_scbond_other	4.971
r_mcbond_it	3.741
r_mcbond_other	3.725
r_angle_refined_deg	1.19
r_angle_other_deg	0.449
r_symmetry_xyhbond_nbd_refined	0.278
r_symmetry_nbd_refined	0.219
r_nbd_other	0.213
r_nbd_refined	0.198
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.158
r_ncsr_local_group_1	0.111
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.069
r_chiral_restr_other	0.01
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1961
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms

Software

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