6RHC | pdb_00006rhc

Fragment AZ-003 binding at the TAZpS89/14-3-3 sigma interface

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, HANGING DROP	7.5	277.15	Protein and peptide were mixed at a 1:2 molar stoichiometry with a final protein concentration of 12 mg/mL in crystallization buffer. This was used during hanging-drop crystallization in a 1:1 ratio with 0.1 M HEPES pH 7.5, 0.2 M CaCl2, 5% glycerol, 2 mM BME and 28% PEG400. Crystals were grown within 10 days at 4 C and fragment soaking was performed on crystals of 10 days and older by adding 0.2 uL of a 100 mM stock solution in dimethyl sulfoxide to 2 uL drops containing multiple crystals.

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.025	α = 90
b = 112.307	β = 90
c = 62.697	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		2018-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033191	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	41.83	99.3	0.113	0.997	11.3	12.8		89802

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.22	97.3		0.937	0.575	2.1	12.8

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 (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	3MHR	1.2	41.83	85244	4541	99.32	0.182	0.18124	0.19	0.19674	0.2	RANDOM	14.636

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]
0.57			-0.17		-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.752
r_dihedral_angle_4_deg	16.417
r_dihedral_angle_3_deg	11.869
r_dihedral_angle_1_deg	5.339
r_long_range_B_refined	4.966
r_long_range_B_other	4.649
r_scangle_other	3.806
r_scbond_it	2.524
r_scbond_other	2.523
r_mcangle_it	2.143
r_mcangle_other	2.142
r_angle_refined_deg	1.912
r_angle_other_deg	1.603
r_mcbond_it	1.425
r_mcbond_other	1.424
r_chiral_restr	0.105
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1869
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	20

Software

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