6Q6R

Recognition of different base tetrads by RHAU: X-ray crystal structure of G4 recognition motif bound to the 3-end tetrad of a DNA G-quadruplex

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	55% methylpentanediol, 40 mM sodium cacodylate (pH 6.0), 80 mM potassium chloride and 12 mM spermine tetrahydrochloride

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.39	α = 90
b = 42.25	β = 99.3
c = 61.404	γ = 90

Symmetry
Space Group	P 1 21 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 2M-F		2016-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	CC (Half)	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	1.5	60.6	99.35	0.079	0.998	8.68	3.827		45681

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.59	98.3		0.763	0.816	1.62	3.62

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	2LK7	1.5	60.6	43297	2308	99.35	0.18832	0.1853	0.24481	RANDOM	26.597

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]
0.71		-0.4	-0.47		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	45.931
r_dihedral_angle_2_deg	25.901
r_sphericity_bonded	20.311
r_dihedral_angle_3_deg	18.268
r_dihedral_angle_4_deg	9.038
r_dihedral_angle_1_deg	7.104
r_long_range_B_refined	6.713
r_mcangle_it	6.596
r_mcangle_other	6.587
r_long_range_B_other	6.411
r_scangle_other	5.975
r_mcbond_it	5.419
r_rigid_bond_restr	5.412
r_mcbond_other	5.351
r_scbond_it	4.85
r_scbond_other	4.849
r_angle_refined_deg	1.947
r_angle_other_deg	1.712
r_chiral_restr	0.136
r_gen_planes_refined	0.024
r_bond_refined_d	0.019
r_gen_planes_other	0.009
r_bond_other_d	0.003
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_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	564
Nucleic Acid Atoms	1364
Solvent Atoms	265
Heterogen Atoms	10

Software

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