4H55 | pdb_00004h55

Crystal structure of Canavalia brasiliensis seed lectin (ConBr) in complex with beta-d-ribofuranose

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	1.8 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.24	α = 90
b = 70.43	β = 90
c = 97.57	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	MAR CCD 130 mm		2006-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.428	LNLS	D03B-MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.15	27.68	90.75			135906	12586	1	1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.15	24.39	12200	11606	594	87.79	0.18528	0.18331	0.2	0.22657	0.24	RANDOM	21.553

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]
0.61			0.78		-1.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.772
r_dihedral_angle_3_deg	16.351
r_dihedral_angle_4_deg	15.463
r_dihedral_angle_1_deg	7.94
r_sphericity_free	7.049
r_scangle_it	4.502
r_sphericity_bonded	3.122
r_scbond_it	3.034
r_angle_refined_deg	2.142
r_mcangle_it	2.126

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.772
r_dihedral_angle_3_deg	16.351
r_dihedral_angle_4_deg	15.463
r_dihedral_angle_1_deg	7.94
r_sphericity_free	7.049
r_scangle_it	4.502
r_sphericity_bonded	3.122
r_scbond_it	3.034
r_angle_refined_deg	2.142
r_mcangle_it	2.126
r_rigid_bond_restr	1.967
r_mcbond_it	1.304
r_chiral_restr	0.134
r_bond_refined_d	0.02
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1775
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms	19

Software

Software
Software Name	Purpose
iMOSFLM	data reduction
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.