3B2N | pdb_00003b2n

Crystal structure of DNA-binding response regulator, LuxR family, from Staphylococcus aureus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	0.1 M Hepes pH 7.5, 1.4 M Sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.898	α = 90
b = 67.898	β = 90
c = 110.662	γ = 120

Symmetry
Space Group	P 61 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	CCD	ADSC QUANTUM 315	X29	2007-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.97900	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.04	50	86.5	0.083	10.2	6.4		15739

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	2.04	2.11	22.9		0.436		1.6	416

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.04	20	9087	436	89.86	0.168	0.165	0.17	0.215	0.22	RANDOM	38.829

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]
0.06	0.03		0.06		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.77
r_dihedral_angle_4_deg	19.578
r_dihedral_angle_3_deg	17.342
r_scbond_it	11.587
r_dihedral_angle_1_deg	6.49
r_scangle_it	6.446
r_mcangle_it	5.504
r_angle_refined_deg	1.661
r_mcbond_it	1.555
r_symmetry_hbond_refined	0.386

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.77
r_dihedral_angle_4_deg	19.578
r_dihedral_angle_3_deg	17.342
r_scbond_it	11.587
r_dihedral_angle_1_deg	6.49
r_scangle_it	6.446
r_mcangle_it	5.504
r_angle_refined_deg	1.661
r_mcbond_it	1.555
r_symmetry_hbond_refined	0.386
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.258
r_nbd_refined	0.212
r_metal_ion_refined	0.153
r_chiral_restr	0.114
r_xyhbond_nbd_refined	0.113
r_bond_refined_d	0.019
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	955
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	1

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
SHELXD	phasing

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.