9IB6 | pdb_00009ib6

Apo form of Tumor necrosis factor-like lectin PLTL from Photorhabdus laumondii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WQ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3.5	293.15	sodium chloride, sodium citrate,

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.501	α = 90
b = 83.501	β = 90
c = 105.577	γ = 120

Symmetry
Space Group	H 3 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 6M		2023-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.97625	BESSY	14.1

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	1.2	42.673	100	1	18.9	19.7		44331

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	1.2	1.26	100		0.842	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	1.2	42.673	44331	2077	99.959	0.158	0.1571	0.1541	0.1815	0.1793	14.847

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]
-0.279	-0.139		-0.279		0.904

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.83
r_lrange_it	12.209
r_dihedral_angle_3_deg	11.991
r_lrange_other	11.357
r_scangle_it	8.525
r_scangle_other	8.519
r_dihedral_angle_1_deg	7.079
r_dihedral_angle_2_deg	6.283
r_scbond_it	6.181
r_scbond_other	6.176
r_mcangle_other	5.553
r_mcangle_it	5.535
r_mcbond_it	4.247
r_mcbond_other	4.09
r_rigid_bond_restr	4.07
r_angle_refined_deg	1.794
r_angle_other_deg	0.635
r_symmetry_xyhbond_nbd_refined	0.234
r_nbd_refined	0.228
r_symmetry_nbd_other	0.201
r_nbd_other	0.178
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.172
r_symmetry_nbd_refined	0.136
r_metal_ion_refined	0.118
r_chiral_restr	0.1
r_symmetry_nbtor_other	0.094
r_symmetry_xyhbond_nbd_other	0.084
r_bond_refined_d	0.012
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	1004
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing