8QEH | pdb_00008qeh

Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AH8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	0.09 M Na Acetate pH 4.5, 2.7 % PEG Smears Medium, 6.3 % MPD, 0.5% n-octyl-beta-D-Glucoside and 10 mM Zinc sulfate heptahydrate

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.644	α = 90
b = 95.813	β = 90
c = 126.801	γ = 90

Symmetry
Space Group	P 21 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 2M-F		2022-01-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1	SLS	X06DA

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	1.43	126.8	100	1	16.5	44		163494

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	1.43	1.45	99.9		0.309	0.7	46.7

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	1.43	63.113	163375	7962	99.98	0.142	0.1399	0.137	0.1804	0.1802	RANDOM	23.784

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]
2.511			-3.419		0.908

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.476
r_dihedral_angle_3_deg	13.088
r_dihedral_angle_2_deg	12.09
r_dihedral_angle_1_deg	6.422
r_lrange_it	4.741
r_lrange_other	4.741
r_scangle_it	4.318
r_scangle_other	4.317
r_rigid_bond_restr	3.488
r_mcangle_it	3.418
r_mcangle_other	3.418
r_scbond_it	3.417
r_scbond_other	3.416
r_mcbond_other	2.609
r_mcbond_it	2.608
r_angle_refined_deg	1.422
r_angle_other_deg	0.518
r_dihedral_angle_other_2_deg	0.387
r_nbd_refined	0.301
r_symmetry_nbd_refined	0.268
r_symmetry_nbd_other	0.2
r_nbd_other	0.194
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.16
r_metal_ion_refined	0.147
r_symmetry_xyhbond_nbd_refined	0.116
r_chiral_restr_other	0.09
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.071
r_symmetry_metal_ion_refined	0.071
r_symmetry_xyhbond_nbd_other	0.01
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5755
Nucleic Acid Atoms
Solvent Atoms	760
Heterogen Atoms	113

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
autoPROC	data scaling
PHASER	phasing