8TON

Crystal Structure of Engineered Mouse Protocadherin-15 EC3-EC7 Connection

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5T4M
experimental model	PDB	5TPK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	15% w/v PEG 20000, 0.1 M Tris HCl pH 8.5, 0.6 uM Spermine Tetrahydrochloride

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.603	α = 90
b = 84.603	β = 90
c = 76.895	γ = 120

Symmetry
Space Group	P 32 2 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 EIGER X 16M		2022-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97918 A	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.94	50	99.9	1	31.9285	11.6		23952

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.94	1.97	100		0.728	1.86	10.4

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	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.94	42.34	23905	1201	99.929	0.186	0.1839	0.2234	42.51

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]
-0.309	-0.154		-0.309		1.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.843
r_dihedral_angle_2_deg	13.212
r_dihedral_angle_3_deg	13.147
r_lrange_other	10.541
r_lrange_it	10.528
r_scangle_it	9.043
r_scangle_other	9.04
r_dihedral_angle_1_deg	7.05
r_scbond_it	6.388
r_scbond_other	6.366
r_mcangle_it	5.641
r_mcangle_other	5.639
r_mcbond_it	4.58
r_mcbond_other	4.577
r_angle_refined_deg	1.713
r_angle_other_deg	0.573
r_metal_ion_refined	0.306
r_nbd_refined	0.239
r_xyhbond_nbd_refined	0.214
r_symmetry_nbd_other	0.199
r_nbd_other	0.192
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.147
r_symmetry_nbd_refined	0.106
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.087
r_chiral_restr_other	0.018
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1776
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing