5TFM | pdb_00005tfm

Crystal Structure of Human Cadherin-23 EC6-8

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.8	277	0.1 M MES pH 6.8, 1.2 M NaCl

Crystal Properties
Matthews coefficient	Solvent content
4.12	70.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.407	α = 90
b = 93.407	β = 90
c = 122.386	γ = 120

Symmetry
Space Group	P 32 1 2

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	ADSC QUANTUM 315		2016-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9792	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.92	80.89	99.9	0.079	17.08	4.2		13518

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.92	2.97	99.9		0.592	2	4.1

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5TFL	2.92	80.89	12825	648	99.85	0.20006	0.19773	0.2	0.24635	0.25	RANDOM	88.416

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]
2.57	1.28		2.57		-8.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.891
r_dihedral_angle_3_deg	16.305
r_dihedral_angle_4_deg	13.538
r_dihedral_angle_1_deg	6.102
r_long_range_B_refined	4.118
r_long_range_B_other	4.096
r_scangle_other	2.633
r_mcangle_it	2.576
r_mcangle_other	2.576
r_mcbond_it	1.542
r_mcbond_other	1.541
r_scbond_it	1.536
r_scbond_other	1.535
r_angle_refined_deg	1.428
r_angle_other_deg	0.895
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2476
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	6

Software

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