7PR8 | pdb_00007pr8

Crystal structure of human heparanase in complex with covalent inhibitor GR109

X-RAY DIFFRACTION

---

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, HANGING DROP		293	0.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.49	α = 90
b = 71.29	β = 95.2
c = 79.07	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		2019-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97933	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.66	39.37	98.6	0.052	0.029	0.999	12.5	4.2		59928

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.66	1.7			1.415	0.789	0.532	1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5e8m	1.66	39.37	59921	3027	98.579	0.168	0.1666	0.18	0.1943	0.2	36.497

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]
2.611		1.759	-2.022		-0.894

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.121
r_dihedral_angle_3_deg	12.135
r_dihedral_angle_4_deg	11.093
r_lrange_it	7.606
r_lrange_other	7.606
r_dihedral_angle_1_deg	6.809
r_scangle_it	6.087
r_scangle_other	6.086
r_scbond_it	4.095
r_scbond_other	4.094
r_mcangle_other	3.933
r_mcangle_it	3.932
r_mcbond_it	2.921
r_mcbond_other	2.917
r_angle_refined_deg	1.694
r_angle_other_deg	1.375
r_chiral_restr	0.28
r_nbd_other	0.248
r_symmetry_xyhbond_nbd_refined	0.217
r_nbd_refined	0.205
r_symmetry_nbd_other	0.178
r_symmetry_nbd_refined	0.175
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.159
r_symmetry_nbtor_other	0.087
r_symmetry_xyhbond_nbd_other	0.04
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3643
Nucleic Acid Atoms
Solvent Atoms	308
Heterogen Atoms	122

Software

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