8XY4 | pdb_00008xy4

Crystal structure of VACV N1 protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8XY1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Tris pH 8.0, 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.86	α = 90
b = 77.86	β = 90
c = 111.39	γ = 120

Symmetry
Space Group	P 61 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		2023-12-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97861	SSRF	BL19U1

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	2.42	42.94	99.9	0.999	24.5	35.7		8116

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	2.42	2.51			0.911

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	FREE R-VALUE	2.42	42.94	8092	405	99.84	0.172	0.1701	0.179	0.2062	0.2058	43.187

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]
0.969	0.484		0.969		-3.143

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.98
r_dihedral_angle_3_deg	12.65
r_dihedral_angle_4_deg	12.452
r_lrange_other	8.442
r_lrange_it	8.436
r_scangle_it	6.615
r_scangle_other	6.613
r_dihedral_angle_1_deg	6.466
r_mcangle_other	5.164
r_mcangle_it	5.162
r_scbond_it	4.81
r_scbond_other	4.778
r_mcbond_it	3.776
r_mcbond_other	3.763
r_angle_refined_deg	1.66
r_angle_other_deg	1.412
r_nbd_refined	0.211
r_nbd_other	0.202
r_symmetry_nbd_other	0.176
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.152
r_symmetry_nbd_refined	0.108
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1014
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms

Software

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