8YHV

Structure of the VP40 from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2M Magnesium chloride hexahydrate 0.1M Tris pH8.5, 25% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.031	α = 90
b = 90.812	β = 97.816
c = 49.22	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	PIXEL	DECTRIS PILATUS 6M		2021-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.000000	SPring-8	BL45XU

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	2.35	48.76	99.1	0.076	10.9	4.1		11721

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	2.35	2.43			0.616

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.35	45.447	11720	566	98.911	0.176	0.1739	0.2229	43.518

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]
0.669		-1.574	-2.31		1.997

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.025
r_dihedral_angle_3_deg	11.203
r_lrange_it	7.611
r_lrange_other	7.6
r_dihedral_angle_1_deg	7.35
r_dihedral_angle_2_deg	6.608
r_scangle_it	4.994
r_scangle_other	4.992
r_mcangle_it	4.401
r_mcangle_other	4.401
r_scbond_it	2.993
r_scbond_other	2.992
r_mcbond_it	2.742
r_mcbond_other	2.737
r_angle_refined_deg	1.215
r_angle_other_deg	0.393
r_symmetry_xyhbond_nbd_refined	0.227
r_nbd_refined	0.196
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.167
r_symmetry_nbd_refined	0.157
r_xyhbond_nbd_refined	0.135
r_symmetry_nbtor_other	0.082
r_nbd_other	0.078
r_chiral_restr	0.054
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1884
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms

Software

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