6L6A | pdb_00006l6a

X-ray structure of human galectin-10 in complex with D-mannose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QKQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1.6 M ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10 % (v/v) 1,4-dioxane

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.83	α = 90
b = 48.83	β = 90
c = 260.94	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU		2018-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.81	19.34	98	0.997	23.1	19.2		17615

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.81	1.86			0.918

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	1QKQ	1.81	19.338	17615	908	98.041	0.19	0.1886	0.2	0.2222	0.22	16.726

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]
-0.004	-0.002		-0.004		0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.9
r_dihedral_angle_4_deg	23.579
r_dihedral_angle_3_deg	14.198
r_dihedral_angle_1_deg	9.076
r_lrange_it	4.193
r_lrange_other	4.162
r_scangle_it	3.121
r_scangle_other	3.119
r_scbond_it	1.986
r_scbond_other	1.986
r_mcangle_it	1.712
r_mcangle_other	1.711
r_angle_refined_deg	1.442
r_angle_other_deg	1.271
r_mcbond_other	1.071
r_mcbond_it	1.07
r_nbd_other	0.177
r_nbd_refined	0.175
r_symmetry_nbd_other	0.168
r_nbtor_refined	0.162
r_symmetry_nbd_refined	0.126
r_symmetry_xyhbond_nbd_refined	0.125
r_xyhbond_nbd_refined	0.092
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1159
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	12

Software

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