3I5L | pdb_00003i5l

Allosteric Modulation of DNA by Small Molecules

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277.15	21% 2-methyl-2,4-pentanediol (MPD), 35 mM calcium acetate, 10 mM Tris pH 7.5 equilibrated in sitting drops against a reservoir of 35% MPD at 4 C. , VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 22.5	α = 66.53
b = 25.14	β = 79.28
c = 29.09	γ = 79.57

Symmetry
Space Group	P 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	CCD				M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97	SSRL	BL12-2

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	1.175	26.472		0.124	12.5	4		19011

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)
	1.175	1.205	90.16		0.154	8.9	4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	AB INITIO PHASING	THROUGHOUT	1.18	26.47	16139	1835	94.55	0.103	0.09902	0.1	0.13764	0.14	RANDOM	5.679

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]
0.03			-0.05	0.04	-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	12.406
r_sphericity_bonded	5.225
r_scangle_it	2.604
r_angle_refined_deg	2.565
r_scbond_it	2.163
r_mcangle_it	2.02
r_rigid_bond_restr	1.725
r_mcbond_it	1.668
r_angle_other_deg	1.481
r_mcbond_other	1.285
r_xyhbond_nbd_refined	0.376
r_symmetry_hbond_refined	0.364
r_nbd_other	0.272
r_nbd_refined	0.238
r_nbtor_refined	0.238
r_symmetry_vdw_other	0.15
r_symmetry_vdw_refined	0.141
r_chiral_restr	0.121
r_nbtor_other	0.089
r_metal_ion_refined	0.082
r_symmetry_metal_ion_refined	0.082
r_gen_planes_refined	0.037
r_bond_refined_d	0.026
r_gen_planes_other	0.02
r_bond_other_d	0.004
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	441
Solvent Atoms	262
Heterogen Atoms	92

Software

Software
Software Name	Purpose
SHELX	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing