8BAC

Crystal structure of human heparanase in complex with competitive inhibitor GD05

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7PRT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.838	α = 90
b = 71.188	β = 98.375
c = 78.628	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 XE 16M		2020-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976254	Diamond	I03

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	2.05	37.677	99.6	0.993	6.2	6.7		30692

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	2.05	2.11			0.672

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	7PRT	2.05	37.677	30674	1488	99.549	0.226	0.2235	0.2674	45.913

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]
2.055		4.443	-5.089		1.655

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.534
r_dihedral_angle_3_deg	16.241
r_dihedral_angle_4_deg	14.252
r_dihedral_angle_1_deg	7.408
r_lrange_it	6.662
r_lrange_other	6.658
r_scangle_other	4.932
r_scangle_it	4.931
r_mcangle_it	4.42
r_mcangle_other	4.419
r_scbond_other	3.211
r_scbond_it	3.21
r_mcbond_it	3.092
r_mcbond_other	3.09
r_angle_refined_deg	1.501
r_angle_other_deg	1.261
r_chiral_restr_other	0.406
r_symmetry_xyhbond_nbd_refined	0.252
r_symmetry_nbd_refined	0.224
r_nbd_refined	0.205
r_symmetry_nbd_other	0.195
r_xyhbond_nbd_refined	0.188
r_nbd_other	0.185
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_other	0.113
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.065
r_xyhbond_nbd_other	0.057
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3627
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	43

Software

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