5EYQ

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

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	Racemic DNA solution*, sodium cacodylate, magnesium chloride, sodium chloride, spermine tetrahydrochloride, MPD *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 L-DNA solution (strands 1,2) and D-DNA solution (strands 3,4) were prepared first with denaturation followed by slow annealing process to ensure proper folding of the duplex formed between the non-self complementary strands. After annealing, the enantiopure solutions were mixed in equimolar ratio and this racemic mixture was used for crystallization.

Crystal Properties
Matthews coefficient	Solvent content
2.32	64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.905	α = 90
b = 68.454	β = 90
c = 34.211	γ = 90

Symmetry
Space Group	P n n a

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	150	PIXEL	DECTRIS PILATUS 200K		2015-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-X	1.54

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	2.3	34.23	96.61	0.045	8.87	1.8		2825

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	2.3	2.38	78.57		0.175	1.34	1.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1BNA	2.3	34.23	2678	147	96.58	0.27591	0.27162	0.35745	RANDOM	37.461

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]
2.18			-6.83		4.65

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	8.307
r_long_range_B_other	8.197
r_scangle_other	7.187
r_scbond_other	4.513
r_scbond_it	4.509
r_angle_refined_deg	1.668
r_angle_other_deg	1.6
r_chiral_restr	0.089
r_gen_planes_refined	0.019
r_bond_refined_d	0.011
r_gen_planes_other	0.002
r_bond_other_d
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	486
Solvent Atoms	19
Heterogen Atoms	1

Software

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