5F5Q | pdb_00005f5q

Crystal structure of Canavalia virosa lectin in complex with alpha-methyl-mannoside

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OW4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	300	Tris-HCl, Ammonium sulphate, Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.25	α = 90
b = 81.74	β = 90
c = 86.93	γ = 90

Symmetry
Space Group	P 21 2 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	PIXEL	DECTRIS PILATUS 2M		2014-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.47	LNLS	W01B-MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.49	36.99	94.5	0.083	0.083	0.095	0.045	0.989	12.2	4.6	14676	14676

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.49	2.63	68.6		0.174	0.074	0.041	0.95	6.2	4	1518

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 (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	2OW4	2.52	36.99	13883	754	97.48	0.1879	0.1845	0.19	0.2509	0.25	RANDOM	27.912

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]
0.03			-0.05		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.079
r_dihedral_angle_4_deg	17.629
r_dihedral_angle_3_deg	14.597
r_dihedral_angle_1_deg	6.895
r_angle_other_deg	3.806
r_mcangle_it	3.44
r_mcbond_it	2.067
r_mcbond_other	2.063
r_angle_refined_deg	1.663
r_chiral_restr	0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.079
r_dihedral_angle_4_deg	17.629
r_dihedral_angle_3_deg	14.597
r_dihedral_angle_1_deg	6.895
r_angle_other_deg	3.806
r_mcangle_it	3.44
r_mcbond_it	2.067
r_mcbond_other	2.063
r_angle_refined_deg	1.663
r_chiral_restr	0.09
r_bond_refined_d	0.014
r_gen_planes_other	0.011
r_gen_planes_refined	0.009
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3588
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	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.