3NBC | pdb_00003nbc

Clitocybe nebularis ricin B-like lectin (CNL) in complex with lactose, crystallized at pH 4.4

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		The starting model was partial structure, obtained by iodine SAD phasing of unpublished data set.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.4	293	0.1M Sodium acetate, 29%(v/v) PEG 550 MME, pH 4.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.789	α = 90
b = 55.898	β = 90
c = 112.414	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	1.01	50	98.4	0.046	17.5	8.7	180640	177749	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	1.01	1.03	94.8		0.403		5.1	8467

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	The starting model was partial structure, obtained by iodine SAD phasing of unpublished data set.	1.01	27.95	180640	177623	8906	98.31	0.159	0.158	0.157	0.15	0.172	0.17	RANDOM	15.61

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]
-0.02			0.06		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.376
r_dihedral_angle_4_deg	10.434
r_dihedral_angle_3_deg	10.038
r_dihedral_angle_1_deg	8.462
r_scangle_it	6.443
r_scbond_it	4.587
r_mcangle_it	3.262
r_rigid_bond_restr	2.289
r_mcbond_it	2.196
r_angle_refined_deg	2.105

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.376
r_dihedral_angle_4_deg	10.434
r_dihedral_angle_3_deg	10.038
r_dihedral_angle_1_deg	8.462
r_scangle_it	6.443
r_scbond_it	4.587
r_mcangle_it	3.262
r_rigid_bond_restr	2.289
r_mcbond_it	2.196
r_angle_refined_deg	2.105
r_chiral_restr	0.319
r_bond_refined_d	0.051
r_gen_planes_refined	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2238
Nucleic Acid Atoms
Solvent Atoms	596
Heterogen Atoms	23

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 U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.