8E51 | pdb_00008e51

Crystal Structure of Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		AlphaFold2 Model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.2 M CaCl2, 0.1 M HEPES pH 7.5, 30% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
3.8	67.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.816	α = 90
b = 75.816	β = 90
c = 242.68	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 EIGER2 X 16M		2022-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97934	APS	24-ID-C

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	2.594	44.599	100	0.975	12.907	28.1		26033

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	2.6	2.64	99.8		0.95	6.53	20.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	AlphaFold2 Model	2.594	44.599	25954	1255	99.792	0.204	0.2019	0.21	0.2424	0.24	62.724

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]
3.185	1.593		3.185		-10.332

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	15.564
r_dihedral_angle_6_deg	15.534
r_dihedral_angle_3_deg	14.654
r_lrange_it	10.799
r_lrange_other	10.798
r_scangle_it	8.709
r_scangle_other	8.708
r_dihedral_angle_1_deg	7.641
r_mcangle_other	7.536
r_mcangle_it	7.535
r_scbond_it	6.544
r_scbond_other	6.423
r_mcbond_it	5.481
r_mcbond_other	5.481
r_angle_refined_deg	1.526
r_angle_other_deg	0.494
r_symmetry_nbd_refined	0.417
r_nbd_other	0.272
r_metal_ion_refined	0.27
r_nbd_refined	0.199
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.157
r_xyhbond_nbd_refined	0.145
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3479
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	15

Software

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