6N2E | pdb_00006n2e

Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6MFO	6MFO, 4AQ8
experimental model	PDB	4AQ8	6MFO, 4AQ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.1 M Imidazole pH 6.8, 46% MPD

Crystal Properties
Matthews coefficient	Solvent content
3.52	65.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.792	α = 90
b = 65.397	β = 99.12
c = 190.015	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER X 16M		2018-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97918	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	2.9	50	93.2	0.115	0.055	12.33	5.2		41847

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	2.95	86.5		0.236		4.4

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 (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	6MFO, 4AQ8	2.9	49.52	37058	1909	92.36	0.22605	0.22464	0.23	0.25332	0.26	RANDOM	75.813

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]
-7.42		-49.81	63.34		-55.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.553
r_dihedral_angle_4_deg	17.897
r_dihedral_angle_3_deg	15.887
r_dihedral_angle_1_deg	8.358
r_long_range_B_refined	2.783
r_long_range_B_other	2.742
r_angle_refined_deg	1.639
r_angle_other_deg	1.28
r_mcangle_it	0.433
r_mcangle_other	0.433
r_scangle_other	0.417
r_scbond_it	0.246
r_scbond_other	0.246
r_mcbond_it	0.235
r_mcbond_other	0.235
r_chiral_restr	0.075
r_gen_planes_refined	0.013
r_bond_refined_d	0.012
r_gen_planes_other	0.002
r_bond_other_d	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	8699
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	18

Software

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