7U88 | pdb_00007u88

Product of 13mer primer with activated G monomer diastereomer 2

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	8.5	293.15	1.5 M Lithium sulfate, 50 mM TRIS pH 8.5, 5% w/v Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.723	α = 90
b = 42.723	β = 90
c = 85.822	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	2.14	50	99.2	0.077	0.082	0.027	1	24.2	9.5		5344

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	2.14	2.18			0.402	0.438	0.166	0.948	2.2	5.7

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	2.14	42.948	4650	239	86.399	0.218	0.2139	0.22	0.2916	0.29	22.402

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]
0.03	0.015		0.03		-0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_other	11.16
r_lrange_it	11.144
r_scangle_other	4.788
r_scangle_it	4.778
r_angle_other_deg	3.537
r_scbond_it	2.764
r_scbond_other	2.762
r_angle_refined_deg	2.603
r_chiral_restr_other	1.454
r_symmetry_nbtor_other	0.277
r_nbtor_refined	0.247
r_symmetry_xyhbond_nbd_refined	0.243
r_symmetry_nbd_other	0.237
r_nbd_other	0.217
r_xyhbond_nbd_refined	0.19
r_symmetry_nbd_refined	0.17
r_chiral_restr	0.168
r_nbd_refined	0.11
r_bond_other_d	0.029
r_symmetry_xyhbond_nbd_other	0.019
r_bond_refined_d	0.018
r_gen_planes_refined	0.012
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	378
Solvent Atoms	49
Heterogen Atoms	334

Software

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