6MEN | pdb_00006men

Crystal structure of a Tylonycteris bat coronavirus HKU4 macrodomain in complex with adenosine diphosphate glucose (ADP-glucose)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6MEA	PDB entry 6MEA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	20-25% PEG3350, 0.1 M HEPES, pH 7.0-7.5, protein:ligand molar ratio 1:10

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.548	α = 73.04
b = 41.691	β = 88.37
c = 60.001	γ = 88.05

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	CCD	RAYONIX MX300-HS	Mirrors	2017-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.5	39.86	99.9	0.129	0.139	0.051	0.995	9.1	7.5		49739			16.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	100		1.284	1.382	0.508	0.721	1.9	7.4

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 (Observed)	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	PDB entry 6MEA	1.5	29.21	47290	2447	99.9	0.1747	0.1729	0.181	0.2086	0.2136	RANDOM	24.8

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]
-0.2	-0.13	-0.02	0.18	-0.01	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.112
r_sphericity_bonded	18.792
r_dihedral_angle_4_deg	15.052
r_dihedral_angle_3_deg	11.359
r_dihedral_angle_1_deg	6.728
r_angle_refined_deg	1.683
r_rigid_bond_restr	1.336
r_angle_other_deg	0.908
r_chiral_restr	0.11
r_bond_refined_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.112
r_sphericity_bonded	18.792
r_dihedral_angle_4_deg	15.052
r_dihedral_angle_3_deg	11.359
r_dihedral_angle_1_deg	6.728
r_angle_refined_deg	1.683
r_rigid_bond_restr	1.336
r_angle_other_deg	0.908
r_chiral_restr	0.11
r_bond_refined_d	0.006
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	2426
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms	76

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.