7VWB

Phloem lectin (PP2) structure -complex with N-Acetyllactosamine (LacNAc)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7VS6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		295	0.1 M MES monohydrate pH 6.0, 22% v/v Polyethylene glycol 400

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.69	α = 90
b = 60.39	β = 99.13
c = 82.98	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	IMAGE PLATE	RIGAKU RAXIS IV++		2020-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU ULTRAX 18	1.5418

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	1.9	30.19	98	0.13	0.97	7	4		28551

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	1.9	2			0.18	0.88

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7VS6	1.9	24.896	28548	1468	98.012	0.22	0.2185	0.2485	13.985

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]
1.64		-0.141	-1.233		-0.344

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.329
r_dihedral_angle_4_deg	14.331
r_dihedral_angle_3_deg	13.002
r_dihedral_angle_1_deg	8.18
r_lrange_it	4.388
r_lrange_other	4.382
r_angle_other_deg	2.35
r_scangle_other	2.202
r_scangle_it	2.201
r_mcangle_other	1.893
r_mcangle_it	1.892
r_angle_refined_deg	1.567
r_scbond_it	1.44
r_scbond_other	1.437
r_mcbond_it	1.192
r_mcbond_other	1.189
r_nbd_other	0.373
r_symmetry_nbd_refined	0.254
r_symmetry_xyhbond_nbd_refined	0.251
r_symmetry_nbd_other	0.225
r_nbd_refined	0.183
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.154
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.073
r_ncsr_local_group_1	0.044
r_symmetry_xyhbond_nbd_other	0.036
r_bond_other_d	0.035
r_chiral_restr_other	0.021
r_gen_planes_other	0.015
r_bond_refined_d	0.01
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2423
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	56

Software

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