9EN6 | pdb_00009en6

Crystal structure of RNA G2C4 repeats - native model pH 6.5

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8QMI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	292	0.08M Magnesium acetate tetrahydrate, 0.05M Sodium cacodylate trihydrate pH 6.5, 30% v/w Polyethylene glycol 4,000

Crystal Properties
Matthews coefficient	Solvent content
1.65	25.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.656	α = 90
b = 45.84	β = 90
c = 51.474	γ = 90

Symmetry
Space Group	C 2 2 21

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		2024-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.72932	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	0.918	25.75	99.9	0.99	17.2	13.3		34769

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.92	0.97	99.8		0.73	1.59

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	FREE R-VALUE	0.918	25.75	34766	1726	99.94	0.119	0.1184	0.13	0.1294	0.13	12.556

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]
0.2			0.05		-0.251

RMS Deviations
Key	Refinement Restraint Deviation
r_rigid_bond_restr	8.598
r_angle_refined_deg	2.749
r_angle_other_deg	2.446
r_scangle_it	2.154
r_scangle_other	2.154
r_lrange_it	1.976
r_lrange_other	1.876
r_scbond_it	1.695
r_scbond_other	1.693
r_nbd_refined	0.423
r_symmetry_xyhbond_nbd_refined	0.325
r_xyhbond_nbd_refined	0.272
r_symmetry_nbd_other	0.252
r_nbtor_refined	0.246
r_nbd_other	0.227
r_symmetry_nbd_refined	0.19
r_chiral_restr	0.157
r_symmetry_nbtor_other	0.094
r_metal_ion_refined	0.036
r_gen_planes_refined	0.035
r_gen_planes_other	0.032
r_bond_refined_d	0.019
r_symmetry_xyhbond_nbd_other	0.012
r_symmetry_metal_ion_refined	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	492
Solvent Atoms	128
Heterogen Atoms	3

Software

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