6TF6 | pdb_00006tf6

Human galectin-3c in complex with a galactose derivative

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		300	20 MG/ML GALECTIN-3C, 100MM NACL, 30 % W/V PEG 4000, 0.4 M NASCN, 10 MM BETA-MERCAPTOETHANOL, 10 MM PHOSHATE, 100 MM MGCL2, 100 MM TRIS/HCL PH 7.5, 4.5 MM LIGAND

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.85	α = 90
b = 57.34	β = 90
c = 62.04	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	MARMOSAIC 225 mm CCD		2013-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3	1.000	MAX II	I911-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.5	31.02	98.8	0.073	12.6	3.6		20755

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.54			0.725

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	3ZSM	1.5	31.02	19717	1038	98.76	0.1194	0.1165	0.1163	0.1743	0.1743	RANDOM	15.578

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]
0.06			-0.25		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	44.662
r_dihedral_angle_2_deg	34.944
r_dihedral_angle_3_deg	13.626
r_sphericity_bonded	10.271
r_dihedral_angle_4_deg	9.069
r_dihedral_angle_1_deg	7.548
r_rigid_bond_restr	4.584
r_angle_refined_deg	2.08
r_angle_other_deg	1.528
r_chiral_restr	0.144
r_bond_refined_d	0.02
r_gen_planes_refined	0.012
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1106
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	42

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing