3QP8 | pdb_00003qp8

Crystal structure of CviR (Chromobacterium violaceum 12472) ligand-binding domain bound to C10-HSL

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QP6	PDB ENTRY 3QP6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9.5	296	100 mM CHES, 1 M sodium citrate, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.461	α = 90
b = 71.613	β = 114.58
c = 77.737	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	CCD	ADSC QUANTUM 315		2008-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25		NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.6	70.71	99.8	0.043	16.678	4		101162	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.6	1.66	99.5		0.397	2.25	3.5

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 (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	PDB ENTRY 3QP6	1.6	70.71	100970	5043	99.63	0.1991	0.1975	0.2	0.2302	0.23	RANDOM	36.043

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]
-0.56		-1.67	-0.48		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.363
r_dihedral_angle_3_deg	13.282
r_dihedral_angle_4_deg	12.508
r_dihedral_angle_1_deg	5.614
r_angle_refined_deg	1.277
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.209
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.165
r_xyhbond_nbd_refined	0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.363
r_dihedral_angle_3_deg	13.282
r_dihedral_angle_4_deg	12.508
r_dihedral_angle_1_deg	5.614
r_angle_refined_deg	1.277
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.209
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.165
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5648
Nucleic Acid Atoms
Solvent Atoms	470
Heterogen Atoms	72

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.