7KUL | pdb_00007kul

DNA 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	6.5	293	0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 50 mM Magnesium Chloride

Crystal Properties
Matthews coefficient	Solvent content
3.05	54.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.443	α = 90
b = 47.443	β = 90
c = 82.803	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	CCD	ADSC QUANTUM 315r		2020-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.00	ALS	8.2.1

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	1.64	50	99	0.075	0.079	0.026	0.985	24.9	9.6		13719

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	1.64	1.67	97.4		0.314	0.339	0.123	0.989	5.3	5.4

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	1.64	50	12116	569	87.581	0.21	0.2079	0.21	0.247	0.26	18.93

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		-0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	4.73
r_lrange_other	4.501
r_angle_other_deg	3.84
r_scangle_it	2.94
r_scangle_other	2.939
r_angle_refined_deg	2.88
r_scbond_it	2.091
r_scbond_other	2.09
r_chiral_restr_other	1.816
r_chiral_restr	0.481
r_nbtor_refined	0.252
r_symmetry_nbtor_other	0.244
r_symmetry_nbd_other	0.222
r_nbd_other	0.169
r_xyhbond_nbd_refined	0.166
r_symmetry_xyhbond_nbd_refined	0.138
r_symmetry_nbd_refined	0.129
r_metal_ion_refined	0.105
r_symmetry_xyhbond_nbd_other	0.095
r_nbd_refined	0.09
r_bond_other_d	0.028
r_bond_refined_d	0.023
r_gen_planes_refined	0.019
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	509
Solvent Atoms	112
Heterogen Atoms	201

Software

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