3EKA

Crystal structure of the complex of hyaluranidase trimer with ascorbic acid at 3.1 A resolution reveals the locations of three binding sites

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C3F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	298	TRIS HCL, SODIUM FORMATE, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.502	α = 90
b = 58.502	β = 90
c = 583.54	γ = 120

Symmetry
Space Group	H 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	203	CCD	MARRESEARCH	MIRROR	2007-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X31	0.803	EMBL/DESY, HAMBURG	X31

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	3.1	50	90	0.11	11.7		6874	6874

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.1	3.15	92		0.434	2.67

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2C3F	3.1	50	6874	6358	516	90	0.212	0.204	0.197	0.234	RANDOM	51.59

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]
4.68	2.34		4.68		-7.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	46.545
r_dihedral_angle_4_deg	25.745
r_dihedral_angle_3_deg	20.869
r_dihedral_angle_1_deg	8.095
r_scangle_it	4.489
r_scbond_it	3.137
r_angle_refined_deg	2.311
r_mcangle_it	2.125
r_mcbond_it	1.672
r_nbtor_refined	0.332

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	46.545
r_dihedral_angle_4_deg	25.745
r_dihedral_angle_3_deg	20.869
r_dihedral_angle_1_deg	8.095
r_scangle_it	4.489
r_scbond_it	3.137
r_angle_refined_deg	2.311
r_mcangle_it	2.125
r_mcbond_it	1.672
r_nbtor_refined	0.332
r_nbd_refined	0.308
r_symmetry_vdw_refined	0.3
r_symmetry_hbond_refined	0.227
r_xyhbond_nbd_refined	0.225
r_chiral_restr	0.12
r_bond_refined_d	0.023
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2515
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	36

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
SCALEPACK	data scaling

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.