9T4Y | pdb_00009t4y

apo form of XN-IL lectin from Xenorhabdus nematophila

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, HANGING DROP	6.5	277	MgSO4, MES pH 6.5, Ethylene glycol, PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.826	α = 90
b = 76.695	β = 90
c = 148.593	γ = 90

Symmetry
Space Group	P 21 21 21

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		2023-10-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9763	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.56	48.14	100	0.192	0.2	0.997	2.56	13.1		83546			14.1

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	1.56	1.64	99.9		1.164	0.773	2.8	13.1

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	1.56	48.137	83447	4396	99.907	0.172	0.171	0.1826	0.1965	0.2042	15.127

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]
-0.276			-0.289		0.565

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.378
r_dihedral_angle_4_deg	27.384
r_dihedral_angle_3_deg	10.139
r_dihedral_angle_1_deg	6.912
r_lrange_it	4.977
r_lrange_other	4.824
r_scangle_it	3.612
r_scangle_other	3.611
r_scbond_it	2.427
r_scbond_other	2.426
r_mcangle_other	2.002
r_mcangle_it	2
r_angle_refined_deg	1.728
r_angle_other_deg	1.474
r_mcbond_it	1.365
r_mcbond_other	1.356
r_nbd_refined	0.208
r_symmetry_nbd_other	0.181
r_symmetry_xyhbond_nbd_refined	0.18
r_nbd_other	0.174
r_nbtor_refined	0.173
r_symmetry_nbd_refined	0.14
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.085
r_metal_ion_refined	0.083
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3789
Nucleic Acid Atoms
Solvent Atoms	580
Heterogen Atoms	69

Software

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