8Q5K | pdb_00008q5k

PqsR coinducer binding domain of Pseudomonas aeruginosa with ligand 2t : 2-(4-(3-((6-chloro-1-(2-methoxyethyl)-1H-benzo[d]imidazol-2-yl)amino)-2-hydroxypropoxy)phenyl)acetonitrile

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JVC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292.15	in 0.1 M Trisodium citrate (pH range 5.8-6.2), 0.2 M Ammonium acetate and MPD (3-8%).

Crystal Properties
Matthews coefficient	Solvent content
4.88	74.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.033	α = 90
b = 119.033	β = 90
c = 115.919	γ = 120

Symmetry
Space Group	P 65 2 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	ADSC QUANTUM 315r		2019-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.75	115.92	99.9	0.988	10.5	10.2		13152

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.83	100		0.816	1.2

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	2.8	103.3	11816	629	99.85	0.22563	0.22242	0.23	0.28479	0.29	RANDOM	100.035

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]
3.68	1.84		3.68		-11.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.468
r_dihedral_angle_4_deg	19.063
r_dihedral_angle_3_deg	18.888
r_long_range_B_refined	12.561
r_long_range_B_other	12.557
r_mcangle_it	8.714
r_mcangle_other	8.699
r_scangle_other	8.158
r_dihedral_angle_1_deg	7.54
r_mcbond_it	5.602
r_mcbond_other	5.591
r_scbond_it	5.035
r_scbond_other	5.032
r_angle_refined_deg	1.298
r_angle_other_deg	1.105
r_chiral_restr	0.049
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1598
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing