9MDW | pdb_00009mdw

16mer self-complementary duplex RNA with all Watson-Crick base pairs

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ND4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	20 % v/v Polyethylene glycol 200, 50 mM HEPES pH 7.5, 200 mM Potassium Chloride, 25 mM Magnesium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.159	α = 90
b = 41.159	β = 90
c = 124.195	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	99	PIXEL	DECTRIS PILATUS3 2M		2024-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97741	ALS	5.0.1

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	1.42	50	100	0.071	0.076	0.027	0.974	4.2	9		7975

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	1.42	1.44	100		0.481	0.511	0.172	0.919	4.2	8.6

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.421	41.398	7944	386	99.611	0.183	0.1812	0.1865	0.2203	0.2211	11.113

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]
0.003	0.002		0.003		-0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	5.974
r_lrange_other	5.753
r_angle_refined_deg	1.977
r_scangle_it	1.802
r_scangle_other	1.801
r_scbond_it	1.261
r_scbond_other	1.259
r_angle_other_deg	0.716
r_nbtor_refined	0.243
r_xyhbond_nbd_refined	0.239
r_symmetry_nbd_other	0.193
r_symmetry_xyhbond_nbd_refined	0.167
r_nbd_other	0.14
r_nbd_refined	0.087
r_symmetry_nbd_refined	0.087
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.078
r_dihedral_angle_other_2_deg	0.05
r_gen_planes_refined	0.028
r_bond_refined_d	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	336
Solvent Atoms	98
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing