4DHM | pdb_00004dhm

Small-molecule inhibitors of 14-3-3 protein-protein interactions from virtual screening

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.7	277	0.095M HEPES Na, 0.19M calcium chloride, 5% glycerol, 28% PEG400, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.2	α = 90
b = 112.28	β = 90
c = 62.44	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	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2011-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.7	19.52	98.2	0.036	30.69	5.58	31580	31580	-3	-3	22.06

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.85	93.1		0.128	9.73		6598

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.7	19.52	31580	31580	1579	100	0.1536	0.1536	0.1518	0.15	0.1872	0.19	RANDOM	17.0087

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]
0.71			-0.18		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.213
r_dihedral_angle_4_deg	15.207
r_dihedral_angle_3_deg	14.157
r_scangle_it	4.94
r_dihedral_angle_1_deg	4.517
r_scbond_it	3.071
r_angle_refined_deg	1.882
r_mcangle_it	1.841
r_mcbond_it	1.112
r_chiral_restr	0.136

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.213
r_dihedral_angle_4_deg	15.207
r_dihedral_angle_3_deg	14.157
r_scangle_it	4.94
r_dihedral_angle_1_deg	4.517
r_scbond_it	3.071
r_angle_refined_deg	1.882
r_mcangle_it	1.841
r_mcbond_it	1.112
r_chiral_restr	0.136
r_bond_refined_d	0.022
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1798
Nucleic Acid Atoms
Solvent Atoms	378
Heterogen Atoms	37

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.