4PXQ

Crystal structure of D-glucuronyl C5-epimerase in complex with heparin hexasaccharide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	16% w/v PEG 3,350, 0.1 M sodium citrate tribasic dehydrate pH 5.6, and 2% v/v Tacsimate pH 5.0., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 152.606	α = 90
b = 200.982	β = 90
c = 46.561	γ = 90

Symmetry
Space Group	P 21 21 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		2013-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97915	SSRF	BL17U

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	2.2	50	100	0.292	9.2	7.3	74069	74069

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	2.2	2.32	100		1.37	2	7.4	10687

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.2	45.43	70293	70265	3728	99.96	0.19568	0.19568	0.19431	0.22177	RANDOM	29.385

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]
-0.39			0.34		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.842
r_dihedral_angle_4_deg	17.51
r_dihedral_angle_3_deg	14.454
r_long_range_B_refined	6.391
r_dihedral_angle_1_deg	5.781
r_mcangle_it	2.457
r_scbond_it	1.973
r_mcbond_it	1.441
r_angle_refined_deg	1.262
r_chiral_restr	0.206

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.842
r_dihedral_angle_4_deg	17.51
r_dihedral_angle_3_deg	14.454
r_long_range_B_refined	6.391
r_dihedral_angle_1_deg	5.781
r_mcangle_it	2.457
r_scbond_it	1.973
r_mcbond_it	1.441
r_angle_refined_deg	1.262
r_chiral_restr	0.206
r_bond_refined_d	0.008
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8252
Nucleic Acid Atoms
Solvent Atoms	813
Heterogen Atoms	210

Software

Software
Software Name	Purpose
HKL-2000	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.