8B0B | pdb_00008b0b

Crystal structure of human heparanase in complex with covalent inhibitor VB151

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% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.442	α = 90
b = 70.846	β = 98.702
c = 78.293	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		2020-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976284	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	1.95	52.312	100	0.989	4.3	5.8		35113

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	1.95	2			0.621

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	1.95	52.312	35090	1711	99.946	0.235	0.2322	0.24	0.2908	0.29	36.986

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]
2.018		1.173	-3.758		1.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.386
r_dihedral_angle_4_deg	19.31
r_dihedral_angle_3_deg	16.745
r_dihedral_angle_1_deg	8.018
r_lrange_it	7.085
r_lrange_other	7.076
r_scangle_it	5.197
r_scangle_other	5.196
r_mcangle_it	4.322
r_mcangle_other	4.321
r_scbond_it	3.351
r_scbond_other	3.35
r_mcbond_other	2.989
r_mcbond_it	2.988
r_angle_refined_deg	1.677
r_angle_other_deg	1.272
r_nbd_other	0.25
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.197
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.17
r_symmetry_nbd_refined	0.167
r_symmetry_xyhbond_nbd_other	0.09
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.067
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	3592
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	65

Software

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