3BR2 | pdb_00003br2

Crystal Structure of the Complex of Dequalinium 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
3.78	67.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 171.601	α = 90
b = 171.601	β = 90
c = 94.329	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 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror	2005-01-14	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	2.9	44	99.8	0.071	5.9	7.5	31749	31649		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)
	2.9	3	100		0.527	1.5	8	3118

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 (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	2.9	43.98	1.5	30176	30083	1597	99.69	0.24957	0.24957	0.24721	0.25	0.29348	0.29	RANDOM	65.166

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]
-0.08			-0.08		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.76
r_dihedral_angle_3_deg	15.368
r_dihedral_angle_4_deg	12.102
r_dihedral_angle_1_deg	4.909
r_scangle_it	1.741
r_mcangle_it	1.599
r_scbond_it	1.1
r_angle_refined_deg	0.881
r_mcbond_it	0.855
r_angle_other_deg	0.787
r_nbd_refined	0.215
r_nbtor_refined	0.191
r_symmetry_vdw_other	0.175
r_symmetry_vdw_refined	0.17
r_nbd_other	0.159
r_symmetry_hbond_refined	0.144
r_xyhbond_nbd_refined	0.121
r_nbtor_other	0.083
r_mcbond_other	0.057
r_chiral_restr	0.051
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
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	5841
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms	159

Software

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