6EEN

Crystal structure of a designer Pentatrico Peptide RNA binding protein, bound to a complex RNA target and featuring an infinite superhelix and microheterogeneity.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M Mg Acetate, 0.05 M MES pH 5.6, 20% MPD

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.347	α = 118.12
b = 51.647	β = 97.21
c = 51.972	γ = 96

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	PIXEL	DECTRIS EIGER X 16M		2017-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.953737	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.01	44.92	97	0.055	0.074	0.049	0.995	9	2		25127

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.01	2.06	90.8		0.305	0.413	0.277	0.786		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	5i9f	2.01	44.92	23919	1207	97.01	0.1862	0.1832	0.2476	RANDOM	32.183

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]
1.99	-1.12	-1.42	-0.06	-0.17	-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.558
r_dihedral_angle_3_deg	20.49
r_dihedral_angle_4_deg	16.019
r_dihedral_angle_1_deg	11.953
r_angle_refined_deg	1.638
r_angle_other_deg	1.206
r_chiral_restr	0.078
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.558
r_dihedral_angle_3_deg	20.49
r_dihedral_angle_4_deg	16.019
r_dihedral_angle_1_deg	11.953
r_angle_refined_deg	1.638
r_angle_other_deg	1.206
r_chiral_restr	0.078
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9776
Nucleic Acid Atoms	765
Solvent Atoms	214
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.