9NIR | pdb_00009nir

Human Ectonucleotide pyrophosphatase/phosphodiesterase family member 3 (ENPP3) inhibitor complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6C02

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.932	α = 90
b = 72.932	β = 90
c = 382.728	γ = 90

Symmetry
Space Group	P 43 21 2

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	Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2	2024-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

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	2.7	37.45	96.7	0.209	0.111	0.968	5.4	4.3		28447			42.3

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	2.7	2.85	98.4		0.852	0.456	0.495	1.8	4.2

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	2.7	30.684	28419	1475	95.497	0.273	0.2702	0.2702	0.3333	0.3331	49.001

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]
-3.18			-3.18		6.361

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.369
r_dihedral_angle_2_deg	12.745
r_dihedral_angle_6_deg	10.569
r_dihedral_angle_1_deg	6.777
r_lrange_it	4.679
r_mcangle_it	1.365
r_scangle_it	1.074
r_angle_refined_deg	1.062
r_mcbond_it	0.731
r_scbond_it	0.566
r_nbtor_refined	0.313
r_symmetry_nbd_refined	0.225
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.18
r_metal_ion_refined	0.121
r_chiral_restr	0.084
r_symmetry_xyhbond_nbd_refined	0.042
r_gen_planes_refined	0.003
r_bond_refined_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6567
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	344

Software

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