3GIJ | pdb_00003gij

Dpo4 extension ternary complex with oxoG(syn)-A(anti) and oxoG(anti)-A(syn) pairs

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GII	PDB entry 3GII

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	100 mM HEPES, 100 mM Calcium acetate, 10% PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.264	α = 90
b = 107.409	β = 100.54
c = 97.867	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315	6144 x 6144 pixel elements with an effective pixel size less than 60x60 micron and resolution of order 90x90 micron	2005-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97942	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.35	20	92.7	0.064	20.1	3.8		40120

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.42	62.4		0.424	1.8

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3GII	2.4	20	38605	1950	94.75	0.212	0.209	0.2052	0.253	0.2504	RANDOM	61.17

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]
-1.55		3.23	-0.04		2.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.895
r_dihedral_angle_4_deg	18.305
r_dihedral_angle_3_deg	16.787
r_dihedral_angle_1_deg	5.191
r_scangle_it	1.835
r_angle_refined_deg	1.601
r_scbond_it	1.402
r_mcangle_it	0.836
r_mcbond_it	0.617
r_nbtor_refined	0.335
r_symmetry_hbond_refined	0.332
r_xyhbond_nbd_refined	0.255
r_nbd_refined	0.243
r_symmetry_vdw_refined	0.236
r_metal_ion_refined	0.184
r_chiral_restr	0.125
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5480
Nucleic Acid Atoms	1180
Solvent Atoms	244
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
HKL-2000	data scaling
AMoRE	phasing