9GV9 | pdb_00009gv9

Structure of Heparinase I from Bacteroides eggerthii in complex with calcium cofactor and delta-UA(1-4)Glc 3, 6, N-Sulphated disaccharide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IKW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M sodium acetate pH 5.0, 2 M ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.80088806	56.1126366

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.59	α = 90
b = 91.563	β = 95.593
c = 73.443	γ = 90

Symmetry
Space Group	C 1 2 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 EIGER2 XE 16M		2023-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.953738	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.715	76.452	90.4	0.165	0.983	7.7	6.7		56421

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.715	1.896			1.045	0.596	1.7

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	1.715	76.452	56418	2859	57.306	0.206	0.2037	0.2049	0.2415	0.2051	19.818

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]
0.061		-0.087	0.019		-0.062

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.643
r_dihedral_angle_6_deg	13.44
r_dihedral_angle_3_deg	11.646
r_dihedral_angle_1_deg	7.579
r_lrange_it	3.318
r_lrange_other	3.181
r_scangle_other	1.451
r_scangle_it	1.45
r_mcangle_it	1.372
r_mcangle_other	1.372
r_angle_refined_deg	1.202
r_scbond_it	0.844
r_scbond_other	0.831
r_mcbond_it	0.786
r_mcbond_other	0.782
r_angle_other_deg	0.417
r_symmetry_nbd_refined	0.219
r_symmetry_xyhbond_nbd_refined	0.212
r_nbd_refined	0.191
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.17
r_nbd_other	0.149
r_symmetry_xyhbond_nbd_other	0.088
r_dihedral_angle_other_2_deg	0.086
r_ncsr_local_group_1	0.081
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.058
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5888
Nucleic Acid Atoms
Solvent Atoms	648
Heterogen Atoms	101

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
MOLREP	phasing