3NBD

Clitocybe nebularis ricin B-like lectin (CNL) in complex with lactose, crystallized at pH 7.1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.1	293	0.085M HEPES sodium, 1.7%(v/v) PEG 400, 2.0M Ammonium sulfate, 19%(w/v) Glycerol, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.119	α = 90
b = 85.08	β = 90
c = 97.629	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	CCD	MAR CCD 165 mm	Collimating and focusing, Pt-coated mirrors	2009-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.033	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.14	23.03	98.3	0.06	11.5	8.5	130730	128514	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.14	1.16	65.6		0.326		5	4260

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3NBC	1.15	23.03	130730	128492	6458	99.51	0.142	0.139	0.138	0.16	RANDOM	15.915

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]
0.33			-0.01		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.059
r_dihedral_angle_4_deg	19.342
r_dihedral_angle_3_deg	10.972
r_dihedral_angle_1_deg	8.566
r_scangle_it	6.829
r_scbond_it	4.863
r_mcangle_it	3.427
r_mcbond_it	2.361
r_angle_refined_deg	2.231
r_rigid_bond_restr	2.226

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.059
r_dihedral_angle_4_deg	19.342
r_dihedral_angle_3_deg	10.972
r_dihedral_angle_1_deg	8.566
r_scangle_it	6.829
r_scbond_it	4.863
r_mcangle_it	3.427
r_mcbond_it	2.361
r_angle_refined_deg	2.231
r_rigid_bond_restr	2.226
r_angle_other_deg	1.689
r_mcbond_other	0.946
r_chiral_restr	0.816
r_bond_refined_d	0.05
r_bond_other_d	0.038
r_gen_planes_refined	0.013
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2238
Nucleic Acid Atoms
Solvent Atoms	535
Heterogen Atoms	71

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
AMoRE	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.