3GIL

Dpo4 extension ternary complex with oxoG(anti)-T(anti) pair

X-RAY DIFFRACTION

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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
3.07	59.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.289	α = 90
b = 110.682	β = 99.22
c = 102.19	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	0.97922	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	2.7	20	99.2	0.113	12.553	4.1		31388

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	2.7	2.78	96.3		0.465	2.5	3.2	2547

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3GIJ	2.71	20	31369	1583	98.75	0.203	0.2	0.259	RANDOM	51.444

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]
-1.09		0.9	0.66		0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.957
r_dihedral_angle_3_deg	17.419
r_dihedral_angle_4_deg	14.682
r_dihedral_angle_1_deg	6.717
r_scangle_it	1.703
r_angle_refined_deg	1.626
r_scbond_it	1.017
r_angle_other_deg	0.893
r_mcangle_it	0.783
r_mcbond_it	0.513
r_nbd_refined	0.212
r_metal_ion_refined	0.194
r_symmetry_hbond_refined	0.191
r_nbtor_refined	0.19
r_nbd_other	0.187
r_symmetry_vdw_other	0.186
r_xyhbond_nbd_refined	0.16
r_symmetry_vdw_refined	0.16
r_chiral_restr	0.131
r_nbtor_other	0.083
r_mcbond_other	0.071
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5480
Nucleic Acid Atoms	1217
Solvent Atoms	119
Heterogen Atoms	68

Software

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