7PRT | pdb_00007prt

Crystal structure of human heparanase in complex with covalent inhibitor CB678

X-RAY DIFFRACTION

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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		293	0.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.808	α = 90
b = 71.622	β = 94.894
c = 78.739	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		2020-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.979524	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	1.7	78	99.8	0.999	11	4.1		56984

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			0.748

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	5e98	1.7	52.951	56910	2800	99.707	0.194	0.1915	0.2001	0.2359	0.2457	38.659

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]
3.639		3.175	-2.883		-1.281

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.159
r_dihedral_angle_4_deg	14.926
r_dihedral_angle_3_deg	14.795
r_lrange_other	7.152
r_lrange_it	7.144
r_dihedral_angle_1_deg	6.905
r_scangle_other	5.599
r_scangle_it	5.598
r_mcangle_it	4.156
r_mcangle_other	4.155
r_scbond_other	3.728
r_scbond_it	3.726
r_mcbond_it	2.993
r_mcbond_other	2.993
r_angle_refined_deg	1.593
r_angle_other_deg	1.299
r_nbd_other	0.233
r_nbd_refined	0.214
r_symmetry_nbd_refined	0.203
r_symmetry_xyhbond_nbd_refined	0.202
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.132
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.072
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	3628
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	117

Software

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