3G6X

Ternary complex of DNA Polymerase iota:DNA:dGTP with an abasic site at the templating position

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FLL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	Crystals grew in 24 hours, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.114	α = 90
b = 98.114	β = 90
c = 202.823	γ = 120

Symmetry
Space Group	P 65 2 2

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 210	Si(111) double-crystal monochromator	2005-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID		APS	17-ID

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	2.08	50	94	0.049	32.6	9.9	35030	33090

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	2.08	2.15	100		0.244	9.9	10.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2FLL	2.08	20	35030	31309	2760	96.14	0.22539	0.22197	0.2647	RANDOM	28.368

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]
0.56	0.28		0.56		-0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.996
r_dihedral_angle_4_deg	24.665
r_dihedral_angle_3_deg	19.444
r_dihedral_angle_1_deg	6.658
r_scangle_it	4.53
r_scbond_it	3.048
r_angle_refined_deg	2.22
r_mcangle_it	1.918
r_mcbond_it	1.079
r_symmetry_vdw_refined	0.315
r_nbtor_refined	0.297
r_symmetry_hbond_refined	0.238
r_nbd_refined	0.236
r_xyhbond_nbd_refined	0.22
r_chiral_restr	0.187
r_bond_refined_d	0.023
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2876
Nucleic Acid Atoms	294
Solvent Atoms	219
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
AMoRE	phasing
CNS	refinement
JDirector	data collection
HKL-2000	data reduction
HKL-2000	data scaling