5LNP

Domain-swapped dimer of human Dishevelled2 DEP domain: monoclinic crystal form crystallised from monomeric fraction

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		unpublished model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.1 M MES, pH=6.5 0.1 M NaCl 0.1 M Li2SO4 23 % PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.583	α = 90
b = 60.181	β = 117.71
c = 66.292	γ = 90

Symmetry
Space Group	P 1 21 1

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 6M-F		2015-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.928190	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.99	42.02	99	0.064	17.3	6.8		29398

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.99	2.06			0.636	2.5	6.6	2884

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	unpublished model	1.99	42.02	27828	1561	99.12	0.1963	0.19351	0.24552	RANDOM	36.899

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]
15.28		8.21	10.18		-25.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.48
r_dihedral_angle_3_deg	17.494
r_dihedral_angle_4_deg	15.241
r_dihedral_angle_1_deg	7.126
r_long_range_B_refined	3.973
r_long_range_B_other	3.972
r_scangle_other	2.372
r_mcangle_it	2.36
r_mcangle_other	2.36
r_angle_refined_deg	1.743
r_scbond_it	1.506
r_scbond_other	1.496
r_mcbond_it	1.491
r_mcbond_other	1.484
r_angle_other_deg	1.046
r_chiral_restr	0.102
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2993
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms	5

Software

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