7RGX | pdb_00007rgx

Crystal structure of human galectin-3 CRD in complex with Methyl 2-O-(2-nitrobenzoyl)-3-O-(4-methylbenzoyl)-b-D-talopyranoside

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NMO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	31% PEG 6000, 100mM MgCL2, 8mM beta mercaptoethanol, 100mM Tris-HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.26	α = 90
b = 57.82	β = 90
c = 61.92	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	ADSC QUANTUM 210r		2012-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

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	1.58	42.23	99.9	0.062	19.7	7.4		16853

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	1.58	1.63			0.275	6.1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2NMO	1.58	30.96	16238	820	92.937	0.188	0.1864	0.2	0.2273	0.23	15.67

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]
0.042			-0.037		-0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.389
r_dihedral_angle_4_deg	21.659
r_dihedral_angle_3_deg	13.618
r_dihedral_angle_1_deg	8.275
r_lrange_it	4.279
r_lrange_other	4.275
r_scangle_it	2.979
r_scangle_other	2.978
r_scbond_it	1.953
r_scbond_other	1.952
r_angle_refined_deg	1.758
r_mcangle_it	1.736
r_mcangle_other	1.735
r_angle_other_deg	1.342
r_mcbond_it	1.252
r_mcbond_other	1.242
r_nbd_other	0.277
r_symmetry_xyhbond_nbd_refined	0.23
r_nbd_refined	0.222
r_symmetry_nbd_other	0.183
r_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.163
r_symmetry_nbd_refined	0.162
r_symmetry_xyhbond_nbd_other	0.157
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.073
r_chiral_restr_other	0.029
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1109
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing