7N4P | pdb_00007n4p

Crystal Structure of Lizard Cadherin-23 EC1-2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WHV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	0.1 M MES pH 6.5 1.1 M CaCl2

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.386	α = 90
b = 43.386	β = 90
c = 296.227	γ = 90

Symmetry
Space Group	P 41 21 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		2016-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97920	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	2.097	50	98.3	0.106	16.65	6.5		17931

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.097	2.14	86		0.589

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	2WHV	2.097	41.671	17565	891	98.475	0.214	0.2108	0.22	0.2665	0.26	40.331

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]
1.921			1.921		-3.843

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.348
r_dihedral_angle_4_deg	17.002
r_dihedral_angle_3_deg	15.058
r_dihedral_angle_1_deg	7.924
r_lrange_it	6.67
r_lrange_other	6.252
r_scangle_other	3.219
r_scangle_it	3.218
r_mcangle_it	2.797
r_mcangle_other	2.796
r_scbond_it	2.011
r_scbond_other	2.008
r_angle_refined_deg	1.857
r_mcbond_other	1.774
r_mcbond_it	1.773
r_angle_other_deg	1.396
r_nbd_refined	0.227
r_symmetry_xyhbond_nbd_refined	0.218
r_metal_ion_refined	0.209
r_xyhbond_nbd_refined	0.207
r_symmetry_nbd_refined	0.201
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.172
r_nbd_other	0.151
r_symmetry_xyhbond_nbd_other	0.091
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.081
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1613
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	9

Software

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