6Z17 | pdb_00006z17

PqsR (MvfR) in complex with antagonist 6

X-RAY DIFFRACTION

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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, HANGING DROP	6	293	100 mM Sodium citrate, 200 mM Ammonium acetate, 5% MPD

Crystal Properties
Matthews coefficient	Solvent content
4.38	71.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.266	α = 90
b = 120.266	β = 90
c = 115.038	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		2019-05-01	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)	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	3.15	60.13	95.7	0.084	0.97	13.9	10.1		8476

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	3.15	3.37			0.803	0.966

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	6q7w, 4jvc	3.15	60.13	8476	406	94.524	0.198	0.1953	0.2	0.2411	0.25	131.882

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]
4.972	2.486		4.972		-16.129

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.295
r_lrange_it	22.707
r_lrange_other	22.705
r_scangle_it	18.016
r_scangle_other	18.008
r_dihedral_angle_3_deg	17.259
r_dihedral_angle_4_deg	16.568
r_mcangle_it	16.014
r_mcangle_other	16.009
r_scbond_it	12.879
r_scbond_other	12.873
r_mcbond_other	11.973
r_mcbond_it	11.968
r_dihedral_angle_1_deg	8.288
r_angle_refined_deg	1.653
r_angle_other_deg	1.294
r_symmetry_nbd_refined	0.328
r_symmetry_xyhbond_nbd_refined	0.306
r_nbd_other	0.246
r_nbd_refined	0.225
r_symmetry_nbd_other	0.205
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.134
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1598
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	21

Software

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