8Q82

Photorhabdus laumondii lectin PLL4 in complex with alpha-methyl-fucoside

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6T96

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	20% PEG4000 20% PEG300 300 mM MgCl2 100 mM MES

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.013	α = 90
b = 82.859	β = 105.357
c = 70.3	γ = 90

Symmetry
Space Group	P 1 21 1

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		2022-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9763	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.95	46.28	99.9	0.045	0.048	0.018	0.9999	21.7	6.9		56507

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.06			0.231	0.251	0.098	0.978	6.8

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	1.95	41.464	56484	2799	99.897	0.206	0.2046	0.2121	0.2399	0.246	33.904

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]
-1.17		-0.025	2.059		-0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.319
r_dihedral_angle_3_deg	13.265
r_dihedral_angle_2_deg	9.427
r_dihedral_angle_1_deg	9.289
r_lrange_it	6.559
r_lrange_other	6.549
r_scangle_it	5.411
r_scangle_other	5.41
r_mcangle_other	4.143
r_mcangle_it	4.142
r_scbond_it	3.726
r_scbond_other	3.726
r_mcbond_it	3.122
r_mcbond_other	3.122
r_angle_refined_deg	1.414
r_angle_other_deg	0.532
r_metal_ion_refined	0.281
r_symmetry_nbd_other	0.203
r_nbd_other	0.193
r_nbtor_refined	0.178
r_nbd_refined	0.177
r_xyhbond_nbd_refined	0.151
r_symmetry_nbtor_other	0.087
r_symmetry_xyhbond_nbd_other	0.086
r_symmetry_nbd_refined	0.076
r_chiral_restr	0.073
r_symmetry_xyhbond_nbd_refined	0.051
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	5226
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	52

Software

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