7KUK | pdb_00007kuk

High resolution 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	4.6	293	0.1 M Sodium acetate trihydrate pH 4.6, 2.0 M Sodium formate, 50 mM Magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.391	α = 90
b = 48.391	β = 90
c = 82.304	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		2020-07-22	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	1.67	50	100	0.038	0.039	0.009	1	91.25	18.5		13505

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	1.67	1.7	99.8		0.328	0.339	0.083	0.996	7	14.8

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	1.67	50	11862	616	87.925	0.203	0.2017	0.21	0.2209	0.22	17.097

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]
0.008	0.004		0.008		-0.026

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	5.398
r_lrange_other	5.189
r_angle_other_deg	3.845
r_scangle_it	3.675
r_scangle_other	3.674
r_angle_refined_deg	3.072
r_scbond_it	2.397
r_scbond_other	2.395
r_chiral_restr_other	1.83
r_chiral_restr	0.504
r_symmetry_xyhbond_nbd_refined	0.261
r_nbtor_refined	0.252
r_symmetry_nbtor_other	0.239
r_xyhbond_nbd_refined	0.232
r_symmetry_nbd_other	0.216
r_nbd_other	0.194
r_symmetry_nbd_refined	0.119
r_nbd_refined	0.104
r_bond_refined_d	0.027
r_bond_other_d	0.027
r_gen_planes_refined	0.021
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	511
Solvent Atoms	108
Heterogen Atoms	195

Software

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