8RU3

Crystal structure of beta-catenin in complex with alpha-helical peptide inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DJS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	300	Crystals grown in 100 mM NaKPO4, 2M NaCl.

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.526	α = 90
b = 91.255	β = 90
c = 112.984	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 EIGER2 XE 16M		2023-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.001	71.013	93.5	0.03	1	11.6	52		18536		1	36.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.002	2.207	61.8		0.124	0.958	1.2	30.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.001	70.991	18535	935	52.451	0.186	0.1839	0.2317	RANDOM	41.859

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]
0.276			0.34		-0.616

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	11.556
r_dihedral_angle_3_deg	10.941
r_lrange_it	8.363
r_lrange_other	8.363
r_scangle_it	6.285
r_scangle_other	6.284
r_dihedral_angle_1_deg	4.419
r_mcangle_it	4.034
r_mcangle_other	4.027
r_dihedral_angle_2_deg	3.989
r_scbond_it	3.985
r_scbond_other	3.984
r_mcbond_it	2.687
r_mcbond_other	2.682
r_angle_refined_deg	0.921
r_angle_other_deg	0.286
r_nbd_refined	0.19
r_symmetry_nbd_other	0.165
r_nbtor_refined	0.158
r_nbd_other	0.15
r_symmetry_nbd_refined	0.137
r_xyhbond_nbd_refined	0.125
r_symmetry_xyhbond_nbd_refined	0.117
r_symmetry_nbtor_other	0.068
r_chiral_restr	0.037
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3976
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
PHASER	phasing
STARANISO	data scaling
xia2.multiplex	data reduction
GDA	data collection