Experiment: 1JUM

Crystal structure of the multidrug binding transcriptional repressor QacR bound to the natural drug berberine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JUS	PDB ENTRY 1JUS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	Ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.98	69.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 174.3	α = 90
b = 174.3	β = 90
c = 96.3	γ = 90

Symmetry
Space Group	P 42 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	IMAGE PLATE	RIGAKU RAXIS IV	yale mirrors	2000-12-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

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	2.98	84.29	85.3	0.105	0.11	10.2	4.1	32199	32199			59

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)
	2.98	3.05	69		0.252	0.3	2.2	3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (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	PDB ENTRY 1JUS	2.98	84.29	28584	28584	2871	92.7	0.236	0.2194	0.284	0.2703	random	59.2

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]
3.08	3.08	-6.16

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	19.8
c_angle_d	1.6
c_improper_angle_d	0.87
c_bond_d	0.104

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6188
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms	135

Software

Software
Software Name	Purpose
CNS	refinement
bioteX	data reduction
bioteX	data scaling
CNS	phasing