9FDB | pdb_00009fdb

Co-crystal structure of Galectin-3 with an inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Internal structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1.8 M Ammonium citrate pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
1.98	38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.486	α = 90
b = 57.886	β = 90
c = 62.417	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	PIXEL	DECTRIS PILATUS 2M-F		2018-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	1.45	31.23	87.2	0.151	0.998	8.4	6.5		19897

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.53			1.44	0.503	1.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.45	31.228	19897	982	87.161	0.182	0.1802	0.1863	0.2099	0.2158	13.496

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]
-0.736			2.47		-1.734

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	13.848
r_lrange_other	13.843
r_dihedral_angle_6_deg	12.572
r_dihedral_angle_3_deg	10.233
r_dihedral_angle_1_deg	7.612
r_dihedral_angle_2_deg	5.593
r_scangle_it	2.446
r_scangle_other	2.445
r_angle_refined_deg	2.435
r_mcangle_other	2.159
r_mcangle_it	2.157
r_scbond_it	1.522
r_scbond_other	1.521
r_rigid_bond_restr	1.316
r_mcbond_it	1.295
r_mcbond_other	1.272
r_angle_other_deg	0.666
r_symmetry_nbd_refined	0.238
r_symmetry_xyhbond_nbd_refined	0.218
r_nbd_refined	0.193
r_symmetry_nbd_other	0.188
r_nbd_other	0.17
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.109
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.055
r_chiral_restr_other	0.024
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1100
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing