9LAD | pdb_00009lad

Crystal structure of the complex between Neuronal Pentraxin 2 (NP2 PTX) and antibody fragment VHH N1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	1% w/v tryptone, 0.001 M sodium azide, 0.05 M HEPES sodium pH7.0, 12% w/v PEG 3,350.

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.574	α = 90
b = 118.234	β = 90
c = 39.464	γ = 90

Symmetry
Space Group	P 21 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 PILATUS3 S 6M		2024-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0000	Photon Factory	BL-5A

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	2.02	46.8	98.2	0.066	0.029	1	31.7	12.5		29010

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	2.02	2.07	80.8		1.051	0.353	0.782	2.4	9.4

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	THROUGHOUT	2.02	46.8	28961	1428	97.858	0.183	0.1816	0.1893	0.2197	0.2278	44.103

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]
1.384			1.785		-3.169

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.032
r_dihedral_angle_3_deg	13.33
r_dihedral_angle_2_deg	10.082
r_dihedral_angle_1_deg	7.802
r_lrange_other	6.732
r_lrange_it	6.728
r_scangle_it	4.797
r_scangle_other	4.796
r_mcangle_it	3.568
r_mcangle_other	3.568
r_scbond_it	3.27
r_scbond_other	3.269
r_mcbond_it	2.531
r_mcbond_other	2.526
r_angle_refined_deg	1.618
r_angle_other_deg	0.548
r_xyhbond_nbd_refined	0.243
r_symmetry_metal_ion_refined	0.23
r_nbd_refined	0.212
r_symmetry_nbd_refined	0.202
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.185
r_nbd_other	0.169
r_metal_ion_refined	0.137
r_symmetry_xyhbond_nbd_refined	0.132
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.073
r_gen_planes_refined	0.008
r_bond_refined_d	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	2543
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	13

Software

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