3BR0 | pdb_00003br0

Crystal Structure of the Complex of Malachite Green 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
3.34	63.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.157	α = 90
b = 104.157	β = 90
c = 97.982	γ = 120

Symmetry
Space Group	P 62

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	KOHZU: Double Crystal Si(111)	2005-08-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.0	ALS	8.2.2

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	2.4	35.7	100	0.085	6.1	7.2	23093	23093		1.7	48.87

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)
	2.4	2.55	100		0.435	1.7	7.4	3362

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	2.42	35.69	21890	21722	1175	99.23	0.21601	0.21601	0.21361	0.2174	0.2609	0.2633	RANDOM	40.946

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]
-0.4	-0.2		-0.4		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.082
r_dihedral_angle_4_deg	31.243
r_dihedral_angle_3_deg	15.122
r_dihedral_angle_1_deg	5.193
r_scangle_it	2.732
r_mcangle_it	2.148
r_scbond_it	1.952
r_mcbond_it	1.234
r_angle_refined_deg	1.056
r_angle_other_deg	0.827
r_symmetry_hbond_refined	0.335
r_symmetry_vdw_refined	0.212
r_nbd_refined	0.201
r_nbtor_refined	0.185
r_nbd_other	0.172
r_xyhbond_nbd_refined	0.157
r_mcbond_other	0.131
r_symmetry_vdw_other	0.127
r_nbtor_other	0.086
r_chiral_restr	0.062
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
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	3031
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	95

Software

Software
Software Name	Purpose
REFMAC	refinement
BOS	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing