8RU4 | pdb_00008ru4

Crystal structure of Human Catenin Beta-1 in complex with stitched peptide inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z6G	MrBump

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	100 mM TRIS pH 8.75, 2%(w/v) PEG-6000, cryoprotected in 30% (w/v) Glucose.

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.567	α = 90
b = 103.617	β = 90
c = 187.923	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		2023-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9212	Diamond	I03

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	2.129	93.961	94.7	0.036	0.999	11.9	13.7		51113		1

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	2.129	2.31	64.9		0.319	0.816	1.3	14.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.13	93.961	51110	2502	72.073	0.203	0.2011	0.2078	0.2403	0.2454	48.028

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]
0.57			-0.827		0.257

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.213
r_lrange_other	14.577
r_lrange_it	14.558
r_dihedral_angle_3_deg	13.3
r_scangle_it	12.041
r_scangle_other	12.04
r_dihedral_angle_other_1_deg	10.5
r_mcangle_other	10.158
r_mcangle_it	10.156
r_scbond_it	8.622
r_scbond_other	8.617
r_mcbond_it	7.354
r_mcbond_other	7.345
r_dihedral_angle_1_deg	4.019
r_dihedral_angle_2_deg	3.207
r_angle_refined_deg	1.196
r_angle_other_deg	0.437
r_nbd_refined	0.197
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.158
r_xyhbond_nbd_refined	0.15
r_symmetry_xyhbond_nbd_refined	0.144
r_nbd_other	0.139
r_ncsr_local_group_1	0.111
r_symmetry_nbd_refined	0.085
r_symmetry_nbtor_other	0.068
r_chiral_restr	0.063
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_symmetry_xyhbond_nbd_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7696
Nucleic Acid Atoms
Solvent Atoms	328
Heterogen Atoms	119

Software

Software
Software Name	Purpose
REFMAC	refinement
GDA	data collection
DIALS	data reduction
STARANISO	data scaling
MrBUMP	phasing