3TT9

Crystal structure of the stable degradation fragment of human plakophilin 2 isoform a (PKP2a) C752R variant

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293.15	reservoir: 22% (w/v) PEG 3350, 75 M malonic acid pH 7.0, protein: 5 mg/mL in 20 mM HEPES, NaOH pH 7.5, 0.1 M NaCl, 3 mM DTT, mix 1:1, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.35	α = 90
b = 63.038	β = 90
c = 74.953	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	CCD	RAYONIX MX-225		2009-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.55	35	99.4			32554	32363		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.59	98.3		2.87

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1XM9	1.55	33.42	-3	32554	30744	1619	100	0.15994	0.15994	0.15822	0.19231	RANDOM	13.662

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]
-0.47			-0.31		0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.115
r_dihedral_angle_4_deg	17.898
r_dihedral_angle_3_deg	12.853
r_dihedral_angle_1_deg	4.922
r_scangle_it	4.466
r_scbond_it	2.754
r_angle_refined_deg	1.595
r_mcangle_it	1.585
r_mcbond_it	0.922
r_chiral_restr	0.127

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.115
r_dihedral_angle_4_deg	17.898
r_dihedral_angle_3_deg	12.853
r_dihedral_angle_1_deg	4.922
r_scangle_it	4.466
r_scbond_it	2.754
r_angle_refined_deg	1.595
r_mcangle_it	1.585
r_mcbond_it	0.922
r_chiral_restr	0.127
r_bond_refined_d	0.015
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1831
Nucleic Acid Atoms
Solvent Atoms	282
Heterogen Atoms	12

Software

Software
Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.