4Z31

Crystal structure of the RC3H2 ROQ domain in complex with stem-loop and double-stranded forms of RNA

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	The protein was diluted to 6.7 mg/ml then mixed with IER3 RNA at a ratio 1:2 before crystallized. 17% PEG10000, 0.1 M Bis-Tris pH6.5, 5% Ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.299	α = 90
b = 174.734	β = 114.12
c = 61.29	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	CCD	ADSC QUANTUM 315		2014-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97924	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.5	50	99.1	0.083	0.09	0.036	8.4	5.9		39757			50.3

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	2.5	2.54	97.6		0.83	0.913	0.377	0.801		5.4	1955

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	4QIK	2.5	50	38676	822	98.91	0.2454	0.2451	0.2592	RANDOM	62.219

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]
-0.1		0.54	-0.84		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.01
r_dihedral_angle_4_deg	14.196
r_dihedral_angle_3_deg	13.394
r_dihedral_angle_1_deg	4.693
r_mcangle_it	3.275
r_mcbond_it	2.017
r_mcbond_other	2.017
r_angle_other_deg	1.218
r_angle_refined_deg	1.094
r_chiral_restr	0.089

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.01
r_dihedral_angle_4_deg	14.196
r_dihedral_angle_3_deg	13.394
r_dihedral_angle_1_deg	4.693
r_mcangle_it	3.275
r_mcbond_it	2.017
r_mcbond_other	2.017
r_angle_other_deg	1.218
r_angle_refined_deg	1.094
r_chiral_restr	0.089
r_bond_refined_d	0.007
r_bond_other_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4534
Nucleic Acid Atoms	1221
Solvent Atoms	40
Heterogen Atoms	3

Software

Software
Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	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.