6EET | pdb_00006eet

Crystal structure of mouse Protocadherin-15 EC9-MAD12

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.1 M HEPES sodium salt, 30% (w/v) MPD, 5% (w/v) PEG4000

Crystal Properties
Matthews coefficient	Solvent content
4.77	74.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.507	α = 90
b = 170.059	β = 90
c = 91.528	γ = 90

Symmetry
Space Group	C 2 2 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		2018-07-02	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	3.2	100	99.5	0.166	14.529	9.8		16630

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	3.2	3.26	94.8		0.808	2.222	4.7

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	6BXZ, 4XHZ	3.23	45.81	15743	790	99.18	0.17854	0.17568	0.18	0.2339	0.24	RANDOM	94.283

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]
3.33			1.9		-5.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.253
r_dihedral_angle_4_deg	19.287
r_dihedral_angle_3_deg	18.554
r_long_range_B_other	12.486
r_long_range_B_refined	12.48
r_scangle_other	10.234
r_mcangle_it	8.767
r_mcangle_other	8.766
r_dihedral_angle_1_deg	8.228
r_scbond_it	6.659
r_scbond_other	6.65
r_mcbond_it	5.993
r_mcbond_other	5.974
r_angle_refined_deg	1.397
r_angle_other_deg	0.809
r_chiral_restr	0.06
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
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	3476
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	108

Software

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