6GKQ | pdb_00006gkq

X-ray structure determined from ex vivo Charcot-Leyden crystal

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	IN CELL		310	Data was collected from ex vivo Charcot-Leyden crystals. Sticky allergic mucin type mucus was obtained from CRSwNP patients undergoing endoscopic sinus surgery. One g of the allergic mucin was cut thoroughly in 10 ml RPMI-1640 (Sigma-Aldrich) containing antibiotics (50 IU/mL penicillin and 50 mg/mL streptomycin; One g of the allergic mucin was cut thoroughly in 10 ml RPMI-1640 (Sigma-Aldrich) containing antibiotics (50 IU/mL penicillin and 50 mg/mL streptomycin; Thermo Fisher Scientific), 0.1 percent BSA (Sigma-Aldrich) and 1 mg/ml Collagen type 2 (Worthington), and further homogenized using a GentleMACS Dissociator (Myltenyi Biotec) and subsequently incubed at 37 degrees for 45 minutes under continuous rotation. After centrifugation the pellet was dissolved in 3 ml PBS containing antibiotics, to which 6 ml Ficoll-Paque (GE Healthcare) was added. After centrifugation at 250g and removal of the supernatant and most of the Ficoll layer, the pellet was dissolved 1:10 in PBS with antibiotics. This precipitation process was repeated 5 more times. The final pellet containing the crystals was resuspended in PBS with antibiotics.

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.941	α = 90
b = 48.941	β = 90
c = 258.337	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	PIXEL	DECTRIS EIGER X 16M		2015-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9763	PETRA III, EMBL c/o DESY	P14 (MX2)

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	2.22	50	99.9	0.31	0.99	7.85	11.86		9972			23.36

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	2.22	2.35	99.1		0.195	0.48	1.29	12.2

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	1LCL	2.3	43.06	8984	896	100	0.191	0.187	0.19	0.232	0.23	RANDOM	29.85

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]
-5.737			-5.737		11.4741

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	17.52
t_omega_torsion	4.27
t_angle_deg	1.13
t_bond_d	0.009
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1110
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	6

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing