7U89 | pdb_00007u89

Product of 14mer primer with activated G monomer diastereomer 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6C8O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	20 mM Magnesium chloride, 50 mM MOPS pH 7.0, 2.0 M Ammonium sulfate, 0.5 mM Spermine

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.204	α = 90
b = 43.204	β = 90
c = 85.638	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	98	CCD	ADSC QUANTUM 315r		2021-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.000	ALS	8.2.2

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	1.65	50	99.6	0.086	0.091	0.029	0.989	21	10.1		11662

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	1.65	1.65	98.9		0.26	0.277	0.093	0.995	5.6	7.8

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	6C8O	1.65	28.562	10238	542	87.437	0.22	0.216	0.22	0.2816	0.29	15.201

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]
-0.003	-0.001		-0.003		0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_other	5.065
r_lrange_it	5.059
r_angle_other_deg	3.474
r_scangle_it	3.214
r_scangle_other	3.213
r_angle_refined_deg	2.984
r_scbond_it	1.955
r_scbond_other	1.955
r_chiral_restr_other	1.62
r_symmetry_nbtor_other	0.263
r_nbtor_refined	0.253
r_symmetry_nbd_other	0.24
r_xyhbond_nbd_refined	0.229
r_nbd_refined	0.219
r_chiral_restr	0.191
r_nbd_other	0.19
r_symmetry_xyhbond_nbd_refined	0.145
r_symmetry_nbd_refined	0.1
r_bond_other_d	0.029
r_bond_refined_d	0.021
r_gen_planes_refined	0.017
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	424
Solvent Atoms	100
Heterogen Atoms	278

Software

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