6Z07 | pdb_00006z07

PqsR (MvfR) in complex with antagonist 12

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 6% MPD

Crystal Properties
Matthews coefficient	Solvent content
4.38	71.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.79	α = 90
b = 120.79	β = 90
c = 114.393	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	2.95	60.47	100	0.089	0.998	12.6	9.6		10879

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	2.95	3.13			1.079	0.917

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	2.95	60.47	10857	528	99.899	0.202	0.1995	0.2	0.2565	0.26	120.825

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]
4.006	2.003		4.006		-12.994

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.883
r_lrange_it	24.169
r_lrange_other	24.168
r_scangle_it	19.096
r_scangle_other	19.088
r_mcangle_it	17.916
r_mcangle_other	17.913
r_dihedral_angle_3_deg	17.727
r_dihedral_angle_4_deg	16.669
r_scbond_it	13.413
r_scbond_other	13.407
r_mcbond_it	13.174
r_mcbond_other	13.163
r_dihedral_angle_1_deg	7.503
r_angle_refined_deg	1.671
r_angle_other_deg	1.262
r_symmetry_nbd_refined	0.431
r_nbd_other	0.415
r_symmetry_xyhbond_nbd_refined	0.232
r_nbd_refined	0.228
r_symmetry_nbd_other	0.202
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.169
r_symmetry_xyhbond_nbd_other	0.169
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.07
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	5
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing