6ZDM

Crystal structure of human heparanase in complex with a N',6O'-bis-sulfated 4-methylumbelliferyl heparan sulfate disaccharide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5E8M

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
2.37	48.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.974	α = 90
b = 70.856	β = 97.128
c = 78.455	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 EIGER X 16M		2019-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	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	1.68	52.4	91	0.045	0.025	0.999	7.8	4.1		24849

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	1.68	1.951	65.7		0.667	0.371	0.692	1.8

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	5e8m	1.714	52.4	24830	1206	47.266	0.182	0.1788	0.2412	39.659

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]
0.18		0.282	-0.527		0.267

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.828
r_dihedral_angle_4_deg	16.227
r_dihedral_angle_3_deg	14.999
r_dihedral_angle_1_deg	7.579
r_lrange_it	7.573
r_lrange_other	7.416
r_scangle_it	5.085
r_scangle_other	4.979
r_mcangle_it	4.718
r_mcangle_other	4.717
r_scbond_it	3.275
r_scbond_other	3.174
r_mcbond_it	3.107
r_mcbond_other	3.107
r_angle_refined_deg	1.574
r_angle_other_deg	1.205
r_symmetry_xyhbond_nbd_refined	0.297
r_symmetry_nbd_refined	0.296
r_nbd_other	0.253
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.199
r_xyhbond_nbd_other	0.195
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.165
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.066
r_symmetry_xyhbond_nbd_other	0.032
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3628
Nucleic Acid Atoms
Solvent Atoms	191
Heterogen Atoms	87

Software

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