8TRI

Crystal Structure of Mouse Cadherin-23 EC25-MAD28 F2894A

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	277	1.25 M Lithium Acetate, 0.1 M MES pH 7.2, 25% glycerol (cryo)

Crystal Properties
Matthews coefficient	Solvent content
6.96	82.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.994	α = 90
b = 164.657	β = 90
c = 183.634	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 EIGER X 16M		2022-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97918	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	3.7	50	99.9	0.981	11.5	10.4		47174

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	3.7	3.76	99.6		0.56	1.96	7

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	3.716	49.563	47043	2329	98.678	0.189	0.1871	0.2294	124.855

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]
4.035			2.426		-6.461

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	40.939
r_lrange_other	40.939
r_scangle_it	36.624
r_scangle_other	36.622
r_mcangle_it	31.456
r_mcangle_other	31.454
r_scbond_it	27.759
r_scbond_other	27.757
r_dihedral_angle_2_deg	26.794
r_dihedral_angle_3_deg	23.336
r_mcbond_it	23.179
r_mcbond_other	23.166
r_dihedral_angle_6_deg	16.871
r_dihedral_angle_1_deg	7.428
r_angle_refined_deg	1.622
r_angle_other_deg	0.499
r_symmetry_nbd_refined	0.422
r_nbd_other	0.36
r_nbd_refined	0.275
r_metal_ion_refined	0.266
r_symmetry_nbd_other	0.238
r_nbtor_refined	0.198
r_xyhbond_nbd_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.106
r_symmetry_nbtor_other	0.093
r_symmetry_xyhbond_nbd_other	0.081
r_chiral_restr	0.061
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10490
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	18

Software

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