Experiment: 5EWB

Racemic crystal structures of Pribnow box consensus promoter sequence (P21/c)

X-RAY DIFFRACTION

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	293	Racemic DNA mixture, sodium cacodylate, sodium chloride, potassium chloride, spermine tetrahydrochloride, MPD For crystallization, four strands were used i.e. (1) d(CGCTATAATGCG) with L-sugars; (2) d(CGCATTATAGCG) with L-sugars; (3) d(CGCTATAATGCG) with D-sugars and (4) d(CGCATTATAGCG) with D-sugars. Enantio-pure DNA solutions were prepared between the non-self complementary strands. Enantiopure DNA solutions were mixed in equimolar ratio and this racemic mixture was used for crystallization.

Crystal Properties
Matthews coefficient	Solvent content
2.35	65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.118	α = 90
b = 67.115	β = 109.22
c = 47.86	γ = 90

Symmetry
Space Group	P 1 21/c 1

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	1.69	42.6	99.3	0.05	13.64	6.56		29346

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	1.69	1.75	97.1		0.515	3.02	6.42

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	1.694	42.6	1.34	29228	1431	99.14	0.3012	0.2988	0.3005	0.3496	0.3521	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	32.169
f_angle_d	1.012
f_chiral_restr	0.052
f_plane_restr	0.011
f_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	972
Solvent Atoms	84
Heterogen Atoms

Software

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