7KUO | pdb_00007kuo

FANA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5UEE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	2.4 M Sodium malonate pH 7.0, 50 mM Magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.072	α = 90
b = 49.072	β = 90
c = 81.254	γ = 120

Symmetry
Space Group	P 3 2 1

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 6M		2020-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.977408	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	2.28	50	100	0.113	0.117	0.114	0.999	29.2	18.8		5536

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	2.28	2.32	100		0.491	0.504	0.027	0.972	7.5	19.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5UEE	2.281	50	5536	298	99.982	0.207	0.2037	0.21	0.263	0.27	27.55

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]
0.012	0.006		0.012		-0.039

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	4.638
r_lrange_other	4.529
r_angle_other_deg	3.786
r_angle_refined_deg	3.366
r_scangle_it	3.247
r_scangle_other	3.246
r_scbond_it	2.296
r_scbond_other	2.294
r_chiral_restr_other	1.733
r_chiral_restr	0.52
r_symmetry_nbtor_other	0.277
r_symmetry_xyhbond_nbd_refined	0.262
r_nbtor_refined	0.246
r_xyhbond_nbd_refined	0.222
r_symmetry_nbd_other	0.221
r_nbd_other	0.177
r_symmetry_nbd_refined	0.144
r_nbd_refined	0.112
r_symmetry_xyhbond_nbd_other	0.038
r_bond_other_d	0.028
r_bond_refined_d	0.027
r_gen_planes_refined	0.014
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	378
Solvent Atoms	47
Heterogen Atoms	327

Software

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