7N86

Crystal Structure of Human Protocadherin-24 EC1-2 Form II

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	0.2 MM NaI 20% PEG3350 CDHR5 EC1-2

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.899	α = 90
b = 86.641	β = 103.458
c = 104.892	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		2020-12-01	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)	CC (Half)	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	3.175	50	96.3	0.987	5.6	3.5		18809

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.175	3.23	89.1		0.277	2.63	2.5

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5CZR	3.175	49.147	18083	862	95.219	0.217	0.2135	0.2896	41.168

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]
-0.375		-1.706	0.913		0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.531
r_dihedral_angle_3_deg	19.808
r_lrange_it	15.899
r_lrange_other	15.899
r_dihedral_angle_4_deg	15.786
r_scangle_it	11.386
r_scangle_other	11.385
r_mcangle_it	8.466
r_mcangle_other	8.465
r_scbond_it	7.766
r_scbond_other	7.766
r_dihedral_angle_1_deg	7.231
r_mcbond_it	5.469
r_mcbond_other	5.467
r_angle_refined_deg	2.02
r_angle_other_deg	1.489
r_nbd_other	0.323
r_metal_ion_refined	0.313
r_symmetry_nbd_refined	0.297
r_symmetry_xyhbond_nbd_refined	0.266
r_nbd_refined	0.244
r_symmetry_nbd_other	0.226
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.153
r_symmetry_xyhbond_nbd_other	0.137
r_symmetry_nbtor_other	0.108
r_chiral_restr	0.073
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6500
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms	187

Software

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