3F8B

Crystal structure of the multidrug binding transcriptional regulator LmrR in drug free state

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ESH	2ESH, 1YYV, 1XMA
experimental model	PDB	1YYV	2ESH, 1YYV, 1XMA
experimental model	PDB	1XMA	2ESH, 1YYV, 1XMA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	30% PEG 1500, 0.1M propionic acid, cacodylate, Bis-Tris propane (PCB buffer), pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2	38.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.669	α = 90
b = 52.695	β = 90
c = 174.998	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	CCD	ADSC QUANTUM 315		2007-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.97	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2	87.499	99.7	0.145	0.145	4.414	7.7	14971	14971		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	99.3		0.503	0.503	1.4	7.8	2148

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2ESH, 1YYV, 1XMA	2	87.37	2	14971	14961	756	99.44	0.221	0.221	0.219	0.272	RANDOM	15.38

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]
-1.39			0.6		0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.144
r_dihedral_angle_4_deg	9.495
r_dihedral_angle_3_deg	8.327
r_scangle_it	2.765
r_scbond_it	1.793
r_dihedral_angle_1_deg	1.627
r_angle_refined_deg	1.433
r_mcangle_it	1.125
r_mcbond_it	0.719
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.144
r_dihedral_angle_4_deg	9.495
r_dihedral_angle_3_deg	8.327
r_scangle_it	2.765
r_scbond_it	1.793
r_dihedral_angle_1_deg	1.627
r_angle_refined_deg	1.433
r_mcangle_it	1.125
r_mcbond_it	0.719
r_nbtor_refined	0.306
r_nbd_refined	0.216
r_symmetry_vdw_refined	0.212
r_symmetry_hbond_refined	0.18
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.123
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1692
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

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 R01GM133198.