3BR6 | pdb_00003br6

Crystal Structure of the Complex of Rhodamine 6G Bound to QacR(E120Q), a Mutant of a Multidrug Binding Transcriptional Repressor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JT6	PDB entry 1jt6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	273	1:1 10mg/ml protein with 2.3M Ammonium sulfate with 100mM Sodium Acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
3.9	68.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 173.099	α = 90
b = 173.099	β = 90
c = 95.576	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	100	CCD	NOIR-1	Rosenbaum-Rock monochromator	2005-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.0	ALS	4.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.2	49.4	93.4	0.059	6.7	5.16	24505	22888		1.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.31	99.7		0.62	0.5	5.2	2324

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB entry 1jt6	3.2	48	23264	21706	1152	93.3	0.23118	0.23118	0.2285	0.23	0.28286	0.29	RANDOM	100.356

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]
1.03			1.03		-2.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.35
r_dihedral_angle_3_deg	16.788
r_dihedral_angle_4_deg	14.674
r_dihedral_angle_1_deg	4.822
r_scangle_it	1.277
r_mcangle_it	1.092
r_angle_refined_deg	0.894
r_scbond_it	0.803
r_angle_other_deg	0.789
r_mcbond_it	0.589
r_nbd_refined	0.215
r_nbtor_refined	0.19
r_nbd_other	0.16
r_symmetry_vdw_refined	0.129
r_xyhbond_nbd_refined	0.12
r_symmetry_vdw_other	0.105
r_nbtor_other	0.086
r_symmetry_hbond_refined	0.076
r_chiral_restr	0.049
r_mcbond_other	0.041
r_bond_refined_d	0.007
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5812
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	128

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
MOLREP	phasing