7XWS | pdb_00007xws

Crystal structure of Wild Type Cypovirus Polyhedra produced by cell-free protein synthesis with small volume

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5GQM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SMALL TUBES		293	cell-free crystallization

Crystal Properties
Matthews coefficient	Solvent content
1.63	24.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.6	α = 90
b = 103.6	β = 90
c = 103.6	γ = 90

Symmetry
Space Group	I 2 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 PILATUS3 6M		2022-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	1	SPring-8	BL32XU

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	1.95	50	100	0.9908	7.3	447.7		13641

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	1.95	1.96	100		0.6707	1.23

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	FREE R-VALUE	5gqm	1.95	42.295	13624	1372	99.985	0.171	0.1659	0.18	0.2157	0.21	20.483

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.904
r_dihedral_angle_4_deg	22.601
r_dihedral_angle_3_deg	12.989
r_dihedral_angle_1_deg	7.657
r_lrange_it	3.223
r_lrange_other	3.172
r_scangle_it	2.426
r_scangle_other	2.422
r_mcangle_it	1.64
r_mcangle_other	1.639
r_scbond_it	1.603
r_scbond_other	1.602
r_angle_refined_deg	1.442
r_angle_other_deg	1.34
r_mcbond_it	1.177
r_mcbond_other	1.172
r_nbd_other	0.235
r_symmetry_nbd_refined	0.223
r_nbd_refined	0.192
r_symmetry_nbd_other	0.173
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.155
r_xyhbond_nbd_refined	0.121
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.071
r_bond_refined_d	0.007
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	2006
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
CrystFEL	data scaling
Coot	model building
XDS	data reduction
PHASER	phasing