6RG2

Photorhabdus laumondii lectin PLL2 in complex with 3-O-methyl-D-glucose

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	11% PEG 4000, 150 mM sodium acetate pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.646	α = 90
b = 56.708	β = 95.33
c = 108.477	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 PILATUS3 2M		2018-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.12	44.84	98.6	0.072	0.998	8.1	3.7		224157			7.939

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	1.12	1.15	98.9		0.768	0.74	1.6	3.5

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.12	44.84	224157	11786	98.59	0.13766	0.13641	0.16099	RANDOM	12.321

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]
0.06		-0.78	-0.63		0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.174
r_dihedral_angle_4_deg	13.22
r_dihedral_angle_3_deg	10.815
r_dihedral_angle_1_deg	7.961
r_rigid_bond_restr	6.166
r_long_range_B_refined	2.924
r_long_range_B_other	2.156
r_angle_refined_deg	1.575
r_angle_other_deg	1.495
r_scangle_other	1.327
r_scbond_it	1.07
r_scbond_other	1.07
r_mcangle_it	0.971
r_mcangle_other	0.971
r_mcbond_it	0.793
r_mcbond_other	0.793
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.004
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5268
Nucleic Acid Atoms
Solvent Atoms	1059
Heterogen Atoms	269

Software

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