7ZV6 | pdb_00007zv6

Crystal Structure of Aichivirus A 2A protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7ZV1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.1M Hepes-NaOH pH7.5 20% PEG1500 0.1M CaCl2

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.456	α = 90
b = 52.776	β = 108.632
c = 61.47	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2012-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87260	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.83	49.76	95.4	0.158	0.116	6.6	3.6		11153

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.83	2.98			0.674	0.583

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	7ZV1	2.83	49.76	11151	543	95.397	0.241	0.24	0.25	0.2507	0.26	42.262

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]
2.583		0.807	-0.497		-2.143

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	11.055
r_dihedral_angle_3_deg	10.791
r_dihedral_angle_2_deg	10.451
r_lrange_it	6.084
r_lrange_other	6.084
r_dihedral_angle_1_deg	5.904
r_mcangle_it	2.617
r_mcangle_other	2.617
r_scangle_it	2.272
r_scangle_other	2.271
r_mcbond_it	1.503
r_mcbond_other	1.503
r_scbond_it	1.351
r_scbond_other	1.351
r_angle_refined_deg	0.716
r_angle_other_deg	0.249
r_symmetry_nbd_other	0.174
r_nbd_refined	0.17
r_nbtor_refined	0.161
r_nbd_other	0.134
r_symmetry_xyhbond_nbd_refined	0.119
r_symmetry_nbd_refined	0.111
r_xyhbond_nbd_refined	0.098
r_symmetry_nbtor_other	0.079
r_ncsr_local_group_3	0.074
r_ncsr_local_group_2	0.067
r_ncsr_local_group_1	0.049
r_chiral_restr	0.034
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2618
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms

Software

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