3W6V | pdb_00003w6v

Crystal structure of the DNA-binding domain of AdpA, the global transcriptional factor, in complex with a target DNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1D5Y	1D5Y, 1BL0
experimental model	PDB	1BL0	1D5Y, 1BL0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.1	277	0.1M sodium HEPES, 10%(v/v) 2-propanol, 16%(w/v) PEG4000, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.66	66.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.51	α = 90
b = 100.64	β = 90
c = 100.91	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 270	diffraction	2010-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.0000	Photon Factory	AR-NE3A

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	2.8	50	98.4	0.077	11.93	5.4	10045	9885	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	2.8	2.87	98.4		0.077	11.93	5.4	10045

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1D5Y, 1BL0	2.95	19.5	8057	8039	399	99.78	0.23787	0.236	0.23	0.2783	0.27	RANDOM	66.487

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]
			-0.1		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.588
r_dihedral_angle_3_deg	21.403
r_dihedral_angle_4_deg	20.724
r_dihedral_angle_1_deg	5.454
r_scangle_it	2.053
r_scbond_it	1.166
r_angle_refined_deg	0.881
r_mcangle_it	0.878
r_mcbond_it	0.443
r_chiral_restr	0.053

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.588
r_dihedral_angle_3_deg	21.403
r_dihedral_angle_4_deg	20.724
r_dihedral_angle_1_deg	5.454
r_scangle_it	2.053
r_scbond_it	1.166
r_angle_refined_deg	0.881
r_mcangle_it	0.878
r_mcbond_it	0.443
r_chiral_restr	0.053
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	896
Nucleic Acid Atoms	650
Solvent Atoms	9
Heterogen Atoms

Software

Software
Software Name	Purpose
ADSC	data collection
XDS	data scaling
REFMAC	refinement
HKL-2000	data reduction

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.