9JQK | pdb_00009jqk

Ebola VP30 and its inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289.15	20% PEG3350 and 200 mM ammonium phosphate dibasic

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.177	α = 72.88
b = 54.042	β = 85.961
c = 83.265	γ = 71.779

Symmetry
Space Group	P 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 EIGER2 S 9M		2023-12-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.97915	SSRF	BL10U2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.29	79.55	95.2	0.099	0.546	2.4	1.7		31319

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	2.29	2.37	95.5		0.547

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.29	48.52	29773	1546	95.14	0.221	0.2184	0.2256	0.2638	0.272	RANDOM	45.408

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]
-0.004	0.007	-0.005	0.014	-0.002	-0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.868
r_lrange_other	10.685
r_lrange_it	10.684
r_dihedral_angle_6_deg	9.794
r_scangle_it	8.982
r_scangle_other	8.981
r_scbond_it	5.984
r_scbond_other	5.982
r_mcangle_it	5.667
r_mcangle_other	5.666
r_dihedral_angle_2_deg	5.076
r_dihedral_angle_1_deg	4.596
r_mcbond_it	4.083
r_mcbond_other	4.073
r_angle_refined_deg	0.62
r_angle_other_deg	0.247
r_nbd_refined	0.201
r_chiral_restr_other	0.191
r_symmetry_nbd_other	0.186
r_symmetry_nbd_refined	0.176
r_nbtor_refined	0.167
r_nbd_other	0.154
r_xyhbond_nbd_refined	0.141
r_symmetry_xyhbond_nbd_refined	0.118
r_symmetry_nbtor_other	0.067
r_chiral_restr	0.033
r_symmetry_xyhbond_nbd_other	0.029
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4040
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	57

Software

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