3QLQ

Crystal structure of Concanavalin A bound to an octa-alpha-mannosyl-octasilsesquioxane cluster

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	294.15	12% PEG 2K MME, 1mM Manganese Chloride, 1mM Calcium Chloride, 100mM HEPES pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.89	α = 90
b = 63.68	β = 93.23
c = 125.8	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	CCD	ADSC QUANTUM 270	TOROIDAL FOCUSING MIRROR	2010-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.95370	NSLS	X6A

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	1.7	31.84	96.1	0.076	13.9	6.2	104059	100001

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	1.7	1.79	88		0.657	2.3	5.7

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	PDB ENTRY 1SCR	1.7	31.84	98996	94987	4961	95.95	0.21942	0.21942	0.21783	0.24832	RANDOM	20.338

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]
-1.18		0.01	3.12		-1.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.03
r_dihedral_angle_4_deg	16.61
r_dihedral_angle_3_deg	14.351
r_dihedral_angle_1_deg	7.703
r_scangle_it	4.417
r_scbond_it	2.942
r_mcangle_it	2.206
r_angle_refined_deg	1.986
r_mcbond_it	1.312
r_angle_other_deg	1.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.03
r_dihedral_angle_4_deg	16.61
r_dihedral_angle_3_deg	14.351
r_dihedral_angle_1_deg	7.703
r_scangle_it	4.417
r_scbond_it	2.942
r_mcangle_it	2.206
r_angle_refined_deg	1.986
r_mcbond_it	1.312
r_angle_other_deg	1.04
r_mcbond_other	0.38
r_chiral_restr	0.116
r_bond_refined_d	0.024
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7111
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	56

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.