5O7U | pdb_00005o7u

Crystal structure of the 7-Fluorotryptophan RSL lectin in complex with Lewis x tetrasaccharide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BT9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	292	60mM divalent, 100 mM buffer 2 pH 7.5, 12.5% peg1K , 12.5% PEG3350 and 12.5% MPD

Crystal Properties
Matthews coefficient	Solvent content
2.31	16.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.152	α = 90
b = 129.152	β = 90
c = 129.152	γ = 90

Symmetry
Space Group	F 2 3

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 315r		2017-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.9799	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	32.3	99.9	0.066	0.015	1	33.2	21.4		63033		2	7.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.15	1.17	100		0.641	0.148	0.962	5.6	20.6

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	2BT9	1.15	32.29	59892	3140	99.86	0.10481	0.10361	0.11	0.12876	0.13	RANDOM	10.991

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.606
r_dihedral_angle_1_deg	24.136
r_sphericity_free	13.205
r_dihedral_angle_3_deg	9.511
r_sphericity_bonded	4.464
r_dihedral_angle_4_deg	4.414
r_rigid_bond_restr	4.075
r_angle_refined_deg	1.963
r_long_range_B_refined	1.923
r_long_range_B_other	1.565
r_scangle_other	1.406
r_scbond_it	1.166
r_scbond_other	1.162
r_angle_other_deg	0.974
r_mcangle_it	0.959
r_mcangle_other	0.959
r_mcbond_other	0.743
r_chiral_restr	0.105
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1378
Nucleic Acid Atoms
Solvent Atoms	279
Heterogen Atoms	158

Software

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