4KNQ | pdb_00004knq

Crystal structure of 1nt-5'-overhanging double-helical CCG-repetitive RNA 20mer complexed with RSS p19

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	291	1.8 M ammonium sulfate, 0.1 M MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.217	α = 90
b = 91.217	β = 90
c = 147.815	γ = 120

Symmetry
Space Group	H 3 2

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 315r			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9395	ESRF	ID14-4

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	1.82	50	98.6	0.139	15.5	5.2		21280

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	1.82	1.89	93.6		0.85		4.4	1981

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.82	15	21136	1083	97.85	0.1834	0.1821	0.19	0.209	0.22	RANDOM	54.4136

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]
1.08	1.08		1.08		-3.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.982
r_dihedral_angle_4_deg	19.467
r_dihedral_angle_3_deg	15.105
r_dihedral_angle_1_deg	6.19
r_mcangle_it	4.561
r_mcbond_it	3.303
r_mcbond_other	3.255
r_angle_refined_deg	1.995
r_angle_other_deg	1.683
r_chiral_restr	0.177

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.982
r_dihedral_angle_4_deg	19.467
r_dihedral_angle_3_deg	15.105
r_dihedral_angle_1_deg	6.19
r_mcangle_it	4.561
r_mcbond_it	3.303
r_mcbond_other	3.255
r_angle_refined_deg	1.995
r_angle_other_deg	1.683
r_chiral_restr	0.177
r_bond_refined_d	0.021
r_gen_planes_refined	0.011
r_bond_other_d	0.007
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	992
Nucleic Acid Atoms	422
Solvent Atoms	144
Heterogen Atoms	15

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.