4XHZ | pdb_00004xhz

Crystal Structure of Human Protocadherin-15 EC8-10

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UBH	3UBH, 1EDH, 3Q2W
experimental model	PDB	1EDH	3UBH, 1EDH, 3Q2W
experimental model	PDB	3Q2W	3UBH, 1EDH, 3Q2W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277.15	0.1M MES (pH6.5), 1.6M NaCl

Crystal Properties
Matthews coefficient	Solvent content
6.76	81.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.929	α = 90
b = 157.929	β = 90
c = 142.898	γ = 120

Symmetry
Space Group	P 63 2 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	PIXEL	DECTRIS PILATUS 6M		2014-10-31	M	SINGLE WAVELENGTH

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

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	2.8	136.77	99.41	0.077	24.95	7.8		26222		-3	73.5

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	2.803	2.876	99.68		0.68	4.09	8.1

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	3UBH, 1EDH, 3Q2W	2.803	136.77	24952	1270	99.43	0.17145	0.17003	0.17	0.19954	0.2	RANDOM	72.383

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]
0.08	0.04		0.08		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.934
r_dihedral_angle_4_deg	16.37
r_dihedral_angle_3_deg	15.358
r_lrange_it	11.585
r_dihedral_angle_1_deg	10.173
r_scangle_it	9.617
r_scbond_it	7.443
r_mcangle_it	7.374
r_mcbond_it	5.319
r_angle_refined_deg	1.247
r_nbtor_refined	0.337
r_ext_dist_refined_d	0.248
r_nbd_refined	0.238
r_symmetry_xyhbond_nbd_refined	0.188
r_symmetry_nbd_refined	0.181
r_xyhbond_nbd_refined	0.145
r_metal_ion_other	0.112
r_chiral_restr	0.072
r_gen_planes_refined	0.012
r_bond_refined_d	0.011
r_metal_ion_refined

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2592
Nucleic Acid Atoms
Solvent Atoms	68
Heterogen Atoms	4

Software

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