7U87 | pdb_00007u87

Product of 13mer 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	6.5	293.15	0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 6.5, 45% v/v (+/-)-2-Methyl-2,4-pentanediol

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.741	α = 90
b = 42.741	β = 90
c = 83.28	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	1.7	50	99.9	0.089	0.094	0.03	1	19.4	9.9		10199

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	1.7	1.73			0.348	0.376	0.139	0.989	2.7	6.5

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	1.701	41.675	9027	469	88.491	0.191	0.1879	0.19	0.2399	0.25	15.893

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]
0.01	0.005		0.01		-0.031

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	7.786
r_lrange_other	7.776
r_scangle_it	3.691
r_scangle_other	3.689
r_angle_other_deg	3.509
r_angle_refined_deg	3.256
r_scbond_it	2.3
r_scbond_other	2.299
r_chiral_restr_other	1.478
r_symmetry_nbtor_other	0.294
r_symmetry_nbd_refined	0.287
r_nbtor_refined	0.25
r_symmetry_nbd_other	0.239
r_chiral_restr	0.197
r_nbd_other	0.188
r_symmetry_xyhbond_nbd_refined	0.185
r_xyhbond_nbd_refined	0.14
r_nbd_refined	0.124
r_metal_ion_refined	0.079
r_bond_refined_d	0.033
r_bond_other_d	0.03
r_gen_planes_refined	0.018
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	378
Solvent Atoms	107
Heterogen Atoms	327

Software

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