7PRB

Crystal structure of Burkholderia pseudomallei heparanase in complex with covalent inhibitor GR109

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	5	293	0.1 M sodium citrate pH 5.0, 14% (w/v) PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.21	α = 90
b = 101.07	β = 90
c = 113.59	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		2019-11-30	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	1.31	66.06	98.5	0.051	0.018	0.999	15.7	8.3		220199

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	1.31	1.34			1.493	0.534	0.682	1.2

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	1.31	66.06	220106	11043	98.361	0.167	0.1657	0.1855	22.799

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]
1.858			-0.637		-1.221

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.701
r_dihedral_angle_4_deg	12.568
r_dihedral_angle_3_deg	12.133
r_dihedral_angle_1_deg	6.809
r_lrange_it	5.616
r_lrange_other	5.342
r_scangle_it	4.305
r_scangle_other	4.304
r_scbond_it	2.878
r_scbond_other	2.877
r_mcangle_other	2.484
r_mcangle_it	2.481
r_angle_refined_deg	1.897
r_mcbond_it	1.811
r_mcbond_other	1.802
r_angle_other_deg	1.607
r_nbd_other	0.326
r_chiral_restr	0.293
r_symmetry_nbd_refined	0.283
r_symmetry_xyhbond_nbd_refined	0.254
r_nbd_refined	0.233
r_xyhbond_nbd_refined	0.21
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_other	0.11
r_symmetry_nbtor_other	0.086
r_ncsr_local_group_1	0.086
r_xyhbond_nbd_other	0.079
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_gen_planes_other	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6291
Nucleic Acid Atoms
Solvent Atoms	991
Heterogen Atoms	90

Software

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