3VW0 | pdb_00003vw0

Crystal Structure of The Dequalinum-bound Form of RamR (Transcriptional Regulator of TetR Family) From Salmonella Typhimurium

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.67	298	0.1M MES, 20mM NaPi, 75mM NaCl, 0.2M Ammonium sulfate, 2mM DTT, 25% PEG 6000, pH 6.67, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 187.345	α = 90
b = 43.551	β = 100.21
c = 106.692	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	CCD	RAYONIX MX225HE		2011-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9000	SPring-8	BL44XU

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	2.6	50	99.8	0.072	11.7	7.4		26448

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	2.6	2.64	100		0.458		7.6	1291

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	2.6	38.15	26359	1334	99.36	0.2263	0.2241	0.23	0.2668	0.27	RANDOM	50.6341

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]
0.09		0.04	-0.1		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.435
r_dihedral_angle_4_deg	20.104
r_dihedral_angle_3_deg	18.905
r_scangle_it	5.387
r_dihedral_angle_1_deg	4.512
r_scbond_it	3.26
r_mcangle_it	2.347
r_angle_refined_deg	1.57
r_mcbond_it	1.227
r_chiral_restr	0.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.435
r_dihedral_angle_4_deg	20.104
r_dihedral_angle_3_deg	18.905
r_scangle_it	5.387
r_dihedral_angle_1_deg	4.512
r_scbond_it	3.26
r_mcangle_it	2.347
r_angle_refined_deg	1.57
r_mcbond_it	1.227
r_chiral_restr	0.102
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5851
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms	88

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

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.