9S2N | pdb_00009s2n

Ternary structure of 14-3-3s, CRAF V263A NS mutant phosphopeptide (pS259), and compound 23 (1083848)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.095 M HEPES pH=7.1-7.7 0.19 M CaCl2 5% glycerol 24-29% PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.026	α = 90
b = 89.368	β = 90
c = 117.851	γ = 90

Symmetry
Space Group	P 2 21 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 4M		2023-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.967697	ESRF	MASSIF-3

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	1.85	58.93	99.8	0.999	19.3	13.4		55674

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	1.85	1.89			0.809

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.85	54.25	55622	2779	99.713	0.21	0.209	0.2189	0.2386	0.2501	RANDOM	20.574

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]
-1.88			1.105		0.775

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.853
r_dihedral_angle_3_deg	13.909
r_lrange_it	6.231
r_lrange_other	6.164
r_dihedral_angle_1_deg	5.685
r_dihedral_angle_2_deg	3.951
r_scangle_it	3.278
r_scangle_other	3.278
r_mcangle_it	2.929
r_mcangle_other	2.929
r_scbond_it	2.024
r_scbond_other	2.023
r_mcbond_it	1.665
r_mcbond_other	1.665
r_angle_refined_deg	1.145
r_angle_other_deg	0.491
r_nbd_refined	0.232
r_nbtor_refined	0.174
r_symmetry_nbd_other	0.159
r_symmetry_nbd_refined	0.152
r_xyhbond_nbd_refined	0.139
r_nbd_other	0.135
r_symmetry_xyhbond_nbd_refined	0.117
r_ncsr_local_group_1	0.113
r_symmetry_nbtor_other	0.069
r_chiral_restr	0.067
r_metal_ion_refined	0.028
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3857
Nucleic Acid Atoms
Solvent Atoms	295
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
MOLREP	phasing