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

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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	0.2289	0.2783	0.2732	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
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