5EZF | pdb_00005ezf

Racemic crystal structures of Pribnow box consensus promoter sequence (Pbca)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FQ2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	Racemic DNA mixture*, HEPES, calcium chloride, PEG400 * For crystallization, we used four strands 1) d(CGCTATAATGCG) with L-sugars 2) d(CGCATTATAGCG) with L-sugars and 3) d(CGCTATAATGCG) with D-sugars 4) d(CGCATTATAGCG) with D-sugars Enantio-pure DNA solutions were prepared first by de-naturation followed by slow cooling down process to ensure proper folding of the hetero-duplex formed between the non-self complementary strands. After slow-annealing, the enantiopure solutions were mixed in equimolar ratio and this racemic DNA mixture was used for crystallization.

Crystal Properties
Matthews coefficient	Solvent content
1.85	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.736	α = 90
b = 39.329	β = 90
c = 65.713	γ = 90

Symmetry
Space Group	P b c a

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 PILATUS 6M		2015-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.9785	SOLEIL	PROXIMA 1

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	1.65	32.86	99.86	0.019	16.92	1.9		12549

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	1.65	1.79	99.76		0.268	2.75	1.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	FREE R-VALUE	1FQ2	1.65	32.856	1.33	12548	611	99.86	0.2973	0.2963	0.2989	0.3167	0.3267	Random selection

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	32.069
f_angle_d	1.626
f_chiral_restr	0.054
f_bond_d	0.007
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	486
Solvent Atoms	52
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing