5E98 | pdb_00005e98

Crystal structure of human heparanase in complex with HepMer M04S02a

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, HANGING 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 = 45.79	α = 90
b = 71.29	β = 95.06
c = 77.92	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		2015-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.979	Diamond	I02

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	1.63	38.45	99.5	0.05	11.7	4		61989

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	1.63	1.67			1.077	0.625	0.465	1.3	3.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5e8m	1.63	38.45	61968	3083	99.454	0.171	0.1697	0.18	0.2063	0.19	from apo structure	35.312

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]
1.14		0.351	-1.096		-0.105

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.901
r_dihedral_angle_4_deg	14.509
r_dihedral_angle_3_deg	13.778
r_lrange_other	8.205
r_lrange_it	8.2
r_dihedral_angle_1_deg	6.696
r_scangle_it	6.442
r_scangle_other	6.439
r_mcangle_it	4.435
r_mcangle_other	4.435
r_scbond_other	4.352
r_scbond_it	4.349
r_mcbond_it	3.203
r_mcbond_other	3.194
r_angle_refined_deg	1.748
r_angle_other_deg	1.412
r_nbd_other	0.302
r_symmetry_nbd_refined	0.269
r_nbd_refined	0.235
r_symmetry_xyhbond_nbd_refined	0.232
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.165
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3686
Nucleic Acid Atoms
Solvent Atoms	243
Heterogen Atoms	54

Software

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