8RMV | pdb_00008rmv

Galectin-3 with a bound inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M HEPES pH 7.5, 1.4 M Sodium citrate (Index/ B8)

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.34	α = 90
b = 57.66	β = 90
c = 61.11	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 EIGER X 4M		2020-03-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.9998	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	1.15	41.938	99.2	0.059	0.999	9.04	2.55		82647

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	1.15	1.22	98.5		1.207	0.403		2.7

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	1.35	41.904	27362	1369	99.956	0.16	0.1583	0.1706	0.1835	0.1874	16.037

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]
-1.08			-0.995		2.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.182
r_dihedral_angle_3_deg	12.12
r_lrange_it	10.447
r_lrange_other	10.446
r_dihedral_angle_1_deg	7.612
r_scangle_it	5.821
r_scangle_other	5.815
r_dihedral_angle_2_deg	4.589
r_mcangle_it	3.996
r_mcangle_other	3.996
r_scbond_it	3.831
r_scbond_other	3.819
r_mcbond_it	2.679
r_mcbond_other	2.666
r_rigid_bond_restr	1.603
r_angle_refined_deg	1.221
r_chiral_restr_other	0.888
r_angle_other_deg	0.665
r_symmetry_nbd_refined	0.205
r_symmetry_nbd_other	0.195
r_nbd_refined	0.184
r_nbtor_refined	0.167
r_nbd_other	0.159
r_symmetry_xyhbond_nbd_refined	0.141
r_xyhbond_nbd_refined	0.108
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.064
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1093
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing