7AEW | pdb_00007aew

14-3-3 sigma bound to bis-phosphorylated aminopeptidase N (APN, CD13) via canonical and non-canonical binding motifs

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MHR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.1 M HEPES pH 7.7 0.19 M CaCl2 5% glycerol 27 % PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.21	α = 90
b = 112.06	β = 90
c = 62.61	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 EIGER2 XE 16M		2019-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.911650	Diamond	I04

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	1.2	45.52	95.8	1	19.82	13.4		86519

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	1.2	1.3			0.854

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	3mhr	1.2	45.516	86512	4326	95.83	0.163	0.1618	0.17	0.1836	0.19	17.766

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]
1.056			-0.366		-0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.958
r_dihedral_angle_4_deg	15.215
r_dihedral_angle_3_deg	13.911
r_lrange_it	5.557
r_lrange_other	5.538
r_dihedral_angle_1_deg	5.419
r_scangle_it	3.529
r_scangle_other	3.529
r_mcangle_it	2.36
r_mcangle_other	2.359
r_scbond_it	2.34
r_scbond_other	2.339
r_angle_refined_deg	1.876
r_angle_other_deg	1.584
r_mcbond_it	1.503
r_mcbond_other	1.503
r_symmetry_xyhbond_nbd_other	0.344
r_symmetry_xyhbond_nbd_refined	0.34
r_symmetry_nbd_refined	0.314
r_nbd_refined	0.26
r_nbd_other	0.254
r_xyhbond_nbd_refined	0.224
r_nbtor_refined	0.184
r_symmetry_nbd_other	0.165
r_symmetry_metal_ion_refined	0.161
r_chiral_restr	0.104
r_metal_ion_refined	0.1
r_symmetry_nbtor_other	0.091
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1946
Nucleic Acid Atoms
Solvent Atoms	426
Heterogen Atoms	5

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement