5E9B

Crystal structure of human heparanase in complex with HepMer M09S05a

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	5.5	293	0.1 M MES [5.5] 0.1 M MgCl2 17% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.32	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.99	α = 90
b = 71.06	β = 95.09
c = 78.29	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 PILATUS 6M		2015-07-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.850	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.88	52.52	99.8	0.06	12.1	4.1		40880

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.88	1.93			1.01

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	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5e8m	1.88	52.52	40866	2036	99.715	0.18	0.1781	0.2172	taken from apo	40.236

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]
1.898		2.229	-2.732		0.431

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.114
r_dihedral_angle_4_deg	15.807
r_dihedral_angle_3_deg	14.304
r_lrange_it	7.635
r_lrange_other	7.634
r_dihedral_angle_1_deg	6.987
r_scangle_it	5.882
r_scangle_other	5.881
r_mcangle_it	4.48
r_mcangle_other	4.479
r_scbond_other	3.873
r_scbond_it	3.87
r_mcbond_it	3.192
r_mcbond_other	3.192
r_angle_refined_deg	1.581
r_angle_other_deg	1.277
r_symmetry_nbd_refined	0.269
r_nbd_other	0.243
r_nbd_refined	0.198
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.117
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.071
r_symmetry_xyhbond_nbd_other	0.012
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3643
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms	102

Software

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