8C30 | pdb_00008c30

Crystal structure of 14-3-3 in complex with PyrinpS242 and a protein/peptide interface fragment

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JC3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	0.19 M CaCl 2 , 5% glycerol, 26% PEG 400, 0.095 M HEPES, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.142	α = 90
b = 111.969	β = 90
c = 62.477	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 PILATUS 6M-F		2020-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033215	PETRA III, DESY	P11

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	1.4	62.48	98.1	0.998	20.5	6.4		55917

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	1.4	1.44			0.948

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	in house	1.4	45.488	55891	2813	98.127	0.181	0.1793	0.19	0.2039	0.21	16.007

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]
0.817			-0.363		-0.454

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.42
r_dihedral_angle_4_deg	13.727
r_dihedral_angle_3_deg	11.66
r_lrange_it	5.409
r_dihedral_angle_1_deg	5.37
r_lrange_other	5.288
r_scangle_it	3.672
r_scangle_other	3.672
r_mcangle_it	2.627
r_mcangle_other	2.626
r_scbond_it	2.512
r_scbond_other	2.512
r_angle_refined_deg	2.004
r_mcbond_it	1.675
r_mcbond_other	1.675
r_angle_other_deg	1.662
r_symmetry_nbd_refined	0.264
r_nbd_refined	0.249
r_nbtor_refined	0.185
r_symmetry_nbd_other	0.182
r_nbd_other	0.175
r_xyhbond_nbd_refined	0.13
r_symmetry_xyhbond_nbd_refined	0.126
r_chiral_restr	0.109
r_symmetry_nbtor_other	0.086
r_metal_ion_refined	0.038
r_symmetry_metal_ion_refined	0.038
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1860
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing