8OHW | pdb_00008ohw

Crystal structure of heparanase from Burkholderia pseudomallei in complex with siastatin B derived inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7PR9

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
2.54	51.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.37	α = 90
b = 104.61	β = 90
c = 113.71	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	0.979330	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	1.27	61.758	99.9	0.999	12.6	8.2		238876

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	1.27	1.29			0.518

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.27	61.758	238766	12173	99.87	0.161	0.1603	0.16	0.1815	0.18	17.891

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]
0.358			0.171		-0.529

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.648
r_dihedral_angle_4_deg	15.555
r_dihedral_angle_3_deg	12.341
r_dihedral_angle_1_deg	6.901
r_lrange_it	5.715
r_lrange_other	5.477
r_scangle_it	4.112
r_scangle_other	4.111
r_scbond_it	2.815
r_scbond_other	2.814
r_mcangle_other	2.408
r_mcangle_it	2.399
r_angle_refined_deg	1.911
r_mcbond_it	1.656
r_mcbond_other	1.634
r_angle_other_deg	1.618
r_symmetry_nbd_refined	0.234
r_nbd_other	0.234
r_nbd_refined	0.223
r_symmetry_nbd_other	0.184
r_symmetry_xyhbond_nbd_refined	0.178
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.092
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6276
Nucleic Acid Atoms
Solvent Atoms	967
Heterogen Atoms	56

Software

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