7T80 | pdb_00007t80

Crystal Structure of Mouse Cadherin-23 EC18-19

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5WJM	5WJM, 5TFK
experimental model	PDB	5TFK	5WJM, 5TFK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	0.2 M (NH4)2SO4 25% w/v PEG 3350 0.1 M Tris-HCl 8.5 pH

Crystal Properties
Matthews coefficient	Solvent content
3.38	63.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.073	α = 90
b = 76.073	β = 90
c = 201.319	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		2021-07-29	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	2.3	67.106	100	0.999	21.28	17.6		30864

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	2.3	2.34	99.9		0.706	2.7	13.4

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	5WJM, 5TFK	2.301	67.106	30796	1549	99.773	0.201	0.1996	0.21	0.2324	0.24	58.004

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]
2.046	1.023		2.046		-6.637

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.459
r_dihedral_angle_4_deg	16.982
r_dihedral_angle_3_deg	15.393
r_lrange_other	10.534
r_lrange_it	10.52
r_dihedral_angle_1_deg	8.262
r_scangle_it	8.145
r_scangle_other	8.144
r_mcangle_it	7.369
r_mcangle_other	7.369
r_scbond_it	5.355
r_scbond_other	5.344
r_mcbond_it	5.094
r_mcbond_other	5.085
r_angle_refined_deg	1.641
r_angle_other_deg	1.216
r_xyhbond_nbd_refined	0.221
r_nbd_refined	0.21
r_symmetry_nbd_refined	0.186
r_nbd_other	0.185
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.152
r_symmetry_xyhbond_nbd_refined	0.135
r_metal_ion_refined	0.111
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.065
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	3274
Nucleic Acid Atoms
Solvent Atoms	68
Heterogen Atoms	8

Software

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