7QUB | pdb_00007qub

EV-A71-3Cpro in complex with inhibitor MG78

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4GHK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	285.15	0.1 M Tris-HCl pH 7.0 + 34% PEG 3350 + 200mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
3.84	67.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.336	α = 90
b = 122.336	β = 90
c = 122.336	γ = 90

Symmetry
Space Group	P 4 3 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 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)	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	2.07	43.25	99.9	0.043	0.999	16.4	38		19792

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	2.07	2.19			0.522

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	4ghk	2.07	43.25	18797	993	99.949	0.193	0.1915	0.2	0.2188	0.22	42.621

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	31.103
r_dihedral_angle_4_deg	18.272
r_dihedral_angle_3_deg	17.575
r_lrange_it	9.497
r_lrange_other	9.483
r_scangle_it	7.968
r_scangle_other	7.964
r_dihedral_angle_1_deg	7.106
r_scbond_it	5.736
r_scbond_other	5.732
r_mcangle_other	4.675
r_mcangle_it	4.674
r_mcbond_it	3.468
r_mcbond_other	3.46
r_dihedral_angle_other_3_deg	2.37
r_angle_refined_deg	1.83
r_angle_other_deg	1.336
r_nbd_refined	0.231
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.165
r_symmetry_nbd_refined	0.165
r_nbd_other	0.146
r_xyhbond_nbd_refined	0.124
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.079
r_symmetry_xyhbond_nbd_refined	0.068
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1413
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	40

Software

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