7LNE | pdb_00007lne

ANA 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, SITTING DROP		293	1.7 M Lithium sulfate, 10 % w/v Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.408	α = 90
b = 43.408	β = 90
c = 86.554	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 EIGER X 16M		2021-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.033175	APS	23-ID-B

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	1.53	50	98.7	0.066	0.073	0.031	0.999	19.9	5.8		14626

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	1.53	1.56	96.9		0.198	0.226	0.106	0.973	6.1	3.4

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	1.53	37.621	14547	756	98.151	0.193	0.1913	0.2	0.2254	0.23	16.202

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]
-0.001	-0.001		-0.001		0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	4.882
r_lrange_other	4.804
r_angle_other_deg	3.85
r_scangle_it	3.16
r_angle_refined_deg	3.091
r_scangle_other	3.05
r_scbond_it	2.141
r_scbond_other	2.044
r_chiral_restr_other	1.751
r_chiral_restr	0.505
r_symmetry_nbtor_other	0.3
r_symmetry_xyhbond_nbd_refined	0.258
r_nbtor_refined	0.252
r_nbd_other	0.247
r_symmetry_nbd_other	0.212
r_xyhbond_nbd_refined	0.206
r_symmetry_nbd_refined	0.176
r_nbd_refined	0.156
r_bond_other_d	0.033
r_bond_refined_d	0.025
r_gen_planes_refined	0.023
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	378
Solvent Atoms	101
Heterogen Atoms	332

Software

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