6TPR | pdb_00006tpr

PqsR (MvfR) bound to inhibitory compound 40

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Q7W	6q7w, 4jvc
experimental model	PDB	4JVC	6q7w, 4jvc

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	100 mM Sodium citrate, 200 mM Ammonium acetate, 3% (v/v) MPD

Crystal Properties
Matthews coefficient	Solvent content
4.38	71.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.754	α = 90
b = 118.754	β = 90
c = 115.242	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	PIXEL	DECTRIS PILATUS 6M-F		2018-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3.2	115.242	99.9	0.234	0.98	6.6	13.5		8390

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.42	99.7		1.392	0.982		14

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6q7w, 4jvc	3.2	115.24	8357	413	99.916	0.208	0.2066	0.21	0.2419	0.24	RANDOM	125.861

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]
4	2		4		-12.976

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.45
r_lrange_it	19.136
r_dihedral_angle_3_deg	18.503
r_dihedral_angle_4_deg	16.792
r_scangle_it	13.701
r_mcangle_it	13.162
r_scbond_it	8.851
r_dihedral_angle_1_deg	8.393
r_mcbond_it	8.357
r_angle_refined_deg	1.289
r_nbtor_refined	0.309
r_nbd_refined	0.278
r_symmetry_nbd_refined	0.272
r_symmetry_xyhbond_nbd_refined	0.175
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.085
r_gen_planes_refined	0.005
r_bond_refined_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1594
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	32

Software

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