7QUW | pdb_00007quw

CVB3-3Cpro in complex with inhibitor MG-78

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VB0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.6	293	0.2 M MgCl2 0.1M Tris-HCl pH 8.6 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.271	α = 90
b = 64.29	β = 115.553
c = 39.85	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 EIGER X 16M		2021-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

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	1.65	35.95	98.1	0.999	15.4	6.7		43026

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	1.65	1.74			0.874

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	2VB0	1.65	33.803	20746	1082	96.56	0.222	0.2192	0.23	0.2791	0.29	50.522

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]
-1.265		2.498	-3.518		1.643

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.913
r_dihedral_angle_3_deg	14.605
r_dihedral_angle_4_deg	12.541
r_lrange_it	8.252
r_lrange_other	8.251
r_dihedral_angle_1_deg	7.601
r_scangle_it	6.474
r_scangle_other	6.471
r_mcangle_it	5.63
r_mcangle_other	5.627
r_scbond_it	4.425
r_scbond_other	4.422
r_mcbond_it	4.181
r_mcbond_other	4.179
r_angle_refined_deg	1.612
r_angle_other_deg	1.221
r_dihedral_angle_other_3_deg	0.4
r_chiral_restr	0.32
r_nbd_refined	0.216
r_xyhbond_nbd_refined	0.193
r_symmetry_xyhbond_nbd_refined	0.179
r_symmetry_nbd_other	0.175
r_symmetry_nbd_refined	0.166
r_nbd_other	0.166
r_nbtor_refined	0.16
r_symmetry_nbtor_other	0.075
r_symmetry_xyhbond_nbd_other	0.011
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	1392
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing