5E8M

Crystal structure of human heparanase

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	0.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.54	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.765	α = 90
b = 70.972	β = 94.17
c = 78.948	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 6M		2015-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.920	Diamond	I02

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	1.75	46.64	100	0.05	12	4.2		49329

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	1.75	1.78	99.8		0.847	1.7	4.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS	THROUGHOUT	1.75	46.64	217940	2647	100	0.16596	0.16411	0.19989	RANDOM	37.357

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]
3.26		1.55	-2.58		-0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.818
r_dihedral_angle_3_deg	13.567
r_dihedral_angle_4_deg	13.188
r_long_range_B_refined	7.27
r_long_range_B_other	7.269
r_dihedral_angle_1_deg	6.389
r_scangle_other	5.68
r_mcangle_it	3.879
r_mcangle_other	3.878
r_scbond_it	3.79
r_scbond_other	3.789
r_mcbond_it	2.859
r_mcbond_other	2.859
r_angle_refined_deg	1.735
r_angle_other_deg	0.987
r_chiral_restr	0.104
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3643
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	143

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
SHELX	phasing