9IB8 | pdb_00009ib8

Tumor necrosis factor-like lectin PLTL from Photorhabdus laumondii in complex with Lewis Y tetrasaccharide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		apoPLTL model, which is released together with this sctructure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293.15	PEG1500, trisodium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.848	α = 90
b = 81.848	β = 90
c = 112.574	γ = 90

Symmetry
Space Group	P 41 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		2024-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.97630	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.6	46.38	100	1	27.7	20		51136

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.69			0.888	3.7

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	1.6	40.958	51062	2537	99.941	0.181	0.1799	0.1894	0.203	0.2081	23.069

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]
0.194			0.194		-0.387

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.121
r_dihedral_angle_3_deg	12.032
r_dihedral_angle_2_deg	9.401
r_dihedral_angle_1_deg	6.934
r_lrange_it	4.944
r_lrange_other	4.944
r_scangle_it	4.477
r_scangle_other	4.476
r_scbond_it	3.151
r_scbond_other	3.15
r_mcangle_it	2.54
r_mcangle_other	2.54
r_mcbond_it	1.975
r_mcbond_other	1.973
r_angle_refined_deg	1.806
r_angle_other_deg	0.623
r_nbd_other	0.292
r_nbd_refined	0.195
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.168
r_symmetry_nbd_refined	0.144
r_xyhbond_nbd_refined	0.134
r_symmetry_nbtor_other	0.095
r_chiral_restr	0.091
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3052
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	92

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
SCALA	data scaling
PHASER	phasing