10ZI | pdb_000010zi

Crystal structure of MrtR bound to 3O-C8 homoserine lactone and tetraethylene glycol

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	imidazole, MES, diethylene glycol, triethylene glycol, tetraethylene glycol, pentaethylene glycol, 2-Methyl-2,4-pentanediol (MPD), PEG 1000, PEG 3350, N-3-oxoctanoyl-L-homoserine lactone, DMSO

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.434	α = 90
b = 35.728	β = 112.13
c = 61.941	γ = 90

Symmetry
Space Group	C 1 2 1

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 PILATUS4 X 4M		2025-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.96546	ESRF	MASSIF-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	1.22	58.56	92.6	0.999	11.5	6.4		70635

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	1.22	1.243	90.5		0.681	0.5	4.5

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	1.22	58.56	66060	3487	91.17	0.15726	0.15539	0.1545	0.19345	0.1928	RANDOM	18.288

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]
-0.05		0.21	-0.18		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	15.193
r_long_range_B_other	12.526
r_dihedral_angle_3_deg	12.378
r_scangle_other	8.787
r_mcangle_other	6.734
r_mcangle_it	6.733
r_dihedral_angle_2_deg	6.292
r_scbond_it	6.112
r_scbond_other	6.11
r_dihedral_angle_1_deg	5.151
r_mcbond_it	4.749
r_mcbond_other	4.723
r_rigid_bond_restr	3.532
r_angle_refined_deg	1.63
r_angle_other_deg	0.593
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_dihedral_angle_4_deg
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1945
Nucleic Acid Atoms
Solvent Atoms	372
Heterogen Atoms	34

Software

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