8OHQ

Crystal structure of human heparanase in complex with competitive inhibitor derrived from siastatin B

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5E98

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
2.48	50.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.11	α = 90
b = 70.92	β = 95.53
c = 78.56	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-F		2015-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.917330	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	1.7	45.938	99.6	0.998	10.8	1.9		55285

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	1.7	1.73			0.598

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.7	45.938	55284	2756	99.566	0.176	0.1743	0.2077	28.937

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]
1.357		0.28	-0.658		-0.739

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.795
r_dihedral_angle_3_deg	14.453
r_dihedral_angle_4_deg	12.75
r_lrange_it	7.13
r_lrange_other	7.12
r_dihedral_angle_1_deg	6.809
r_scangle_it	5.372
r_scangle_other	5.371
r_mcangle_it	3.917
r_mcangle_other	3.916
r_scbond_it	3.514
r_scbond_other	3.514
r_mcbond_it	2.607
r_mcbond_other	2.607
r_angle_refined_deg	1.65
r_angle_other_deg	1.478
r_chiral_restr_other	0.494
r_symmetry_nbd_refined	0.354
r_symmetry_xyhbond_nbd_refined	0.259
r_nbd_refined	0.21
r_symmetry_nbd_other	0.192
r_nbd_other	0.192
r_xyhbond_nbd_other	0.171
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.142
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.005
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3640
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	107

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing