6Z5K | pdb_00006z5k

PqsR (MvfR) in complex with antagonist 18

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	100 mM Sodium citrate, 200 mM Ammonium acetate and 5% MPD

Crystal Properties
Matthews coefficient	Solvent content
4.38	71.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.911	α = 90
b = 118.911	β = 90
c = 115.464	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 EIGER X 16M		2019-05-02	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)	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	115.46	92.4	0.061	0.997	16.6	9		7628

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			0.398	0.972

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4JVC, 6Q7W	3.201	76.972	7592	401	90.467	0.206	0.2035	0.21	0.2613	0.27	134.248

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]
4.477	2.238		4.477		-14.523

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.781
r_dihedral_angle_3_deg	15.685
r_lrange_it	13.053
r_lrange_other	13.05
r_dihedral_angle_4_deg	11.028
r_mcangle_it	9.168
r_mcangle_other	9.16
r_scangle_it	8.719
r_scangle_other	8.715
r_dihedral_angle_1_deg	6.651
r_mcbond_it	5.835
r_mcbond_other	5.826
r_scbond_it	5.313
r_scbond_other	5.311
r_angle_refined_deg	1.236
r_angle_other_deg	1.067
r_symmetry_nbd_refined	0.222
r_nbd_refined	0.192
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.154
r_nbd_other	0.153
r_xyhbond_nbd_refined	0.122
r_symmetry_xyhbond_nbd_refined	0.08
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.038
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1598
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	23

Software

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