8B0C

Crystal structure of human heparanase in complex with covalent inhibitor VB158

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5E8M

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
2.49	50.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.976	α = 90
b = 71.441	β = 95.45
c = 78.261	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 EIGER2 X 16M		2021-07-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9762	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.1	52.71	100	0.998	8.3	5.7		29584

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16			0.592	0.8

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5e8m	2.1	52.71	29568	1439	99.929	0.204	0.2015	0.2621	47.328

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]
2.149		2.116	-2.335		-0.214

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.842
r_dihedral_angle_3_deg	16.471
r_dihedral_angle_4_deg	13.176
r_lrange_other	7.987
r_lrange_it	7.984
r_dihedral_angle_1_deg	7.72
r_scangle_other	6.388
r_scangle_it	6.387
r_mcangle_it	5.576
r_mcangle_other	5.576
r_scbond_other	4.394
r_scbond_it	4.392
r_mcbond_it	4.077
r_mcbond_other	4.075
r_angle_refined_deg	1.668
r_angle_other_deg	1.262
r_nbd_other	0.281
r_symmetry_nbd_refined	0.233
r_nbd_refined	0.217
r_symmetry_nbd_other	0.181
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.142
r_symmetry_xyhbond_nbd_refined	0.09
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.069
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3610
Nucleic Acid Atoms
Solvent Atoms	68
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing