4U36 | pdb_00004u36

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FNZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3.5	293	Citric acid buffers, ammonium sulphate.

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.076	α = 90
b = 85.808	β = 90
c = 129.057	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	PSI PILATUS 6M		2013-12-14	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	1.398	71.455	99.5	0.059	0.064	0.025	18.6	6.5	61513	61513

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	1.4	1.47	96.9		0.268	0.268	0.115	2.8	6.3	8641

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	1FNZ	1.4	71.46	61844	3117	99.47	0.179	0.178	0.19	0.1968	0.2	RANDOM	13.798

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]
0.58			0.73		-1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.829
r_dihedral_angle_3_deg	12.201
r_sphericity_free	11.106
r_dihedral_angle_4_deg	8.643
r_rigid_bond_restr	8.135
r_dihedral_angle_1_deg	5.919
r_sphericity_bonded	3.917
r_angle_other_deg	2.827
r_angle_refined_deg	1.547
r_mcbond_it	1.435

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.829
r_dihedral_angle_3_deg	12.201
r_sphericity_free	11.106
r_dihedral_angle_4_deg	8.643
r_rigid_bond_restr	8.135
r_dihedral_angle_1_deg	5.919
r_sphericity_bonded	3.917
r_angle_other_deg	2.827
r_angle_refined_deg	1.547
r_mcbond_it	1.435
r_mcangle_it	1.433
r_mcbond_other	1.382
r_chiral_restr	0.098
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1777
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	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.