4XTP | pdb_00004xtp

Crystal structure of a recombinant Vatairea macrocarpa seed lectin complexed with Tn antigen

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4U2A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3.5	293	Cubic-like crystals

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.093	α = 90
b = 86.024	β = 90
c = 128.877	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	100	PIXEL	DECTRIS PILATUS 6M		2013-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.915	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.968	71.55	97.7	0.112	0.122	0.049	10	6.2		22033

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)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.97	2.07	85.3		0.521	0.521	0.229	1.3	5.8	2762

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	4U2A	1.97	71.55	20674	1123	96.68	0.2007	0.1979	0.21	0.2544	0.2	RANDOM	29.233

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]
-1.93			2.67		-0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.165
r_dihedral_angle_3_deg	15.041
r_sphericity_free	9.363
r_dihedral_angle_4_deg	6.997
r_dihedral_angle_1_deg	6.254
r_rigid_bond_restr	4.989
r_sphericity_bonded	4.748
r_mcbond_it	2.694
r_mcbond_other	2.668
r_mcangle_it	2.614

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.165
r_dihedral_angle_3_deg	15.041
r_sphericity_free	9.363
r_dihedral_angle_4_deg	6.997
r_dihedral_angle_1_deg	6.254
r_rigid_bond_restr	4.989
r_sphericity_bonded	4.748
r_mcbond_it	2.694
r_mcbond_other	2.668
r_mcangle_it	2.614
r_angle_other_deg	2.359
r_angle_refined_deg	1.463
r_chiral_restr	0.088
r_bond_refined_d	0.014
r_gen_planes_other	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1811
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	71

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building
iMOSFLM	data reduction

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.