8VAX | pdb_00008vax

Cadmium catalyzed primer extension product with 14mer primer and mixed phosphorothioate activated G monomer

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5L00

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	35% w/v 1,6-Hexanediol, 50 mM TRIS pH 8.5 75 mM Magnesium sulfate.

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.471	α = 90
b = 43.471	β = 90
c = 83.887	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		2023-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 2.0.1	1.03579	ALS	2.0.1

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	1.417	50	91.5	0.095	0.101	0.035	0.994	19.6	7.2		16509

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	1.42	1.44	56.4		0.286	0.35	0.198	0.834	3.4	2.4

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	THROUGHOUT	1.417	41.944	16343	841	90.188	0.177	0.1749	0.1799	0.218	0.2241	12.69

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	5.689
r_lrange_other	5.488
r_scangle_it	4.189
r_scangle_other	4.017
r_angle_other_deg	3.763
r_angle_refined_deg	2.868
r_scbond_it	2.586
r_scbond_other	2.317
r_chiral_restr_other	1.786
r_xyhbond_nbd_refined	0.333
r_symmetry_nbtor_other	0.264
r_nbtor_refined	0.251
r_symmetry_xyhbond_nbd_refined	0.211
r_symmetry_nbd_other	0.192
r_nbd_other	0.182
r_chiral_restr	0.135
r_symmetry_nbd_refined	0.103
r_nbd_refined	0.084
r_dihedral_angle_other_2_deg	0.057
r_metal_ion_refined	0.036
r_bond_other_d	0.029
r_gen_planes_refined	0.022
r_bond_refined_d	0.019
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	644
Solvent Atoms	183
Heterogen Atoms	51

Software

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