3ZSK | pdb_00003zsk

Crystal structure of Human Galectin-3 CRD with glycerol bound at 0.90 angstrom resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZSJ	PDB ENTRY 3ZSJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		30% PEG 4000, 0.1M MGCL2, 0.008M BETA MERCAPTOETHANOL, 0.1M TRIS-HCL, PH 7.5, 0.4M NASCN

Crystal Properties
Matthews coefficient	Solvent content
1.79	31.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.83	α = 90
b = 58.2	β = 90
c = 62.54	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	MARRESEARCH		2009-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-5		MAX II	I911-5

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	0.9	20	95.8	0.04	20.4	5.89		93342		1

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	0.9	0.92	87.3		0.79	2.1	4.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	FREE R-VALUE	PDB ENTRY 3ZSJ	0.9	20	88644	4695	95.8	0.1323	0.1326		0.14	0.1501	0.14	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
29	996.62	1363.35

RMS Deviations
Key	Refinement Restraint Deviation
s_zero_chiral_vol	0.103
s_non_zero_chiral_vol	0.101
s_approx_iso_adps	0.085
s_similar_adp_cmpnt	0.046
s_anti_bump_dis_restr	0.036
s_from_restr_planes	0.035
s_angle_d	0.032
s_bond_d	0.015
s_rigid_bond_adp_cmpnt	0.006
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1109
Nucleic Acid Atoms
Solvent Atoms	262
Heterogen Atoms	12

Software

Software
Software Name	Purpose
SHELXL-97	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	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.