7PR9

Crystal structure of Burkholderia pseudomallei heparanase in complex with covalent inhibitor VL166

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M sodium citrate pH 5.0, 14% (w/v) PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.87	α = 90
b = 104.137	β = 90
c = 113.988	γ = 90

Symmetry
Space Group	P 21 21 21

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		2019-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97950	Diamond	I04

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	1.34	79.89	98.9	0.058	0.022	0.999	13.4	7.6		210296

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	1.34	1.37			1.215	0.607	0.565	1.1

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5bwi	1.34	77.002	209958	10582	98.651	0.177	0.1762	0.1989	21.494

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]
0.946			-0.041		-0.905

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.298
r_dihedral_angle_4_deg	16.709
r_dihedral_angle_3_deg	12.485
r_dihedral_angle_1_deg	6.785
r_lrange_it	5.531
r_lrange_other	5.308
r_scangle_it	3.868
r_scangle_other	3.868
r_mcangle_other	2.739
r_mcangle_it	2.737
r_scbond_it	2.63
r_scbond_other	2.63
r_mcbond_it	1.945
r_mcbond_other	1.933
r_angle_refined_deg	1.807
r_angle_other_deg	1.555
r_nbd_other	0.267
r_symmetry_xyhbond_nbd_refined	0.243
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.179
r_symmetry_nbd_refined	0.178
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.171
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.084
r_ncsr_local_group_1	0.084
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6282
Nucleic Acid Atoms
Solvent Atoms	992
Heterogen Atoms	78

Software

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