3CL5 | pdb_00003cl5

Structure of coronavirus hemagglutinin-esterase in complex with 4,9-O-diacetyl sialic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		wild-type structure of Hemagglutinin-esterase

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.04 M KH2PO4, 16% (w/v) PEG 8000, 20% (w/v) glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.78	67.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.24	α = 90
b = 89.24	β = 90
c = 280.38	γ = 120

Symmetry
Space Group	P 65 2 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	CCD	ADSC QUANTUM 315		2006-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.0723	ESRF	ID23-1

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	1.8	77.4	97.2	0.092	25.5	20.7	60345	60283		-3.7	27.1

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	1.8	1.9	86.6		0.866	3.5	19	7667

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	wild-type structure of Hemagglutinin-esterase	1.8	50	57018	57018	3043	96.05	0.1712	0.17031	0.18	0.1883	0.2	RANDOM	25.046

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]
0.28	0.14		0.28		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.994
r_dihedral_angle_4_deg	15.925
r_dihedral_angle_3_deg	12.665
r_dihedral_angle_1_deg	6.754
r_scangle_it	2.974
r_scbond_it	1.858
r_angle_refined_deg	1.334
r_angle_other_deg	1.282
r_mcangle_it	1.134
r_mcbond_it	0.625

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.994
r_dihedral_angle_4_deg	15.925
r_dihedral_angle_3_deg	12.665
r_dihedral_angle_1_deg	6.754
r_scangle_it	2.974
r_scbond_it	1.858
r_angle_refined_deg	1.334
r_angle_other_deg	1.282
r_mcangle_it	1.134
r_mcbond_it	0.625
r_mcbond_other	0.164
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2860
Nucleic Acid Atoms
Solvent Atoms	281
Heterogen Atoms	131

Software

Software
Software Name	Purpose
REFMAC	refinement
DNA	data collection
XDS	data reduction
SCALA	data scaling
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.