8QS3 | pdb_00008qs3

Ternary structure of 14-3-3s, C-RAF 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	3IQV

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
2.86	57.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.685	α = 90
b = 89.262	β = 90
c = 116.969	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 PILATUS 6M		2023-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.885603	ESRF	ID23-1

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	1.6	116.97	98.2	0.999	16.6	13.1		83028

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	1.6	1.63			0.727	1.8

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 (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	1.6	70.96	78774	4186	98.2	0.18475	0.18397	0.222	0.19922	0.2326	RANDOM	24.435

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]
-0.02			0.84		-0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.292
r_long_range_B_refined	7.489
r_dihedral_angle_2_deg	7.455
r_long_range_B_other	7.395
r_dihedral_angle_1_deg	5.202
r_scangle_other	5.099
r_scbond_other	3.309
r_scbond_it	3.308
r_mcangle_it	2.827
r_mcangle_other	2.827
r_mcbond_it	1.914
r_mcbond_other	1.914
r_angle_refined_deg	1.084
r_angle_other_deg	0.451
r_chiral_restr	0.052
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3812
Nucleic Acid Atoms
Solvent Atoms	446
Heterogen Atoms	56

Software

Software
Software Name	Purpose
PDB-REDO	refinement
autoPROC	data reduction
Aimless	data scaling
MOLREP	phasing