2FLL | pdb_00002fll

Ternary complex of human DNA polymerase iota with DNA and dTTP

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5		pH 6.5, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.329	α = 90
b = 98.329	β = 90
c = 202.186	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						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	2.6	50	99.7	0.059	34.5	7	18517	18496

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB code 2AZL	2.6	50	18517	16057	1376	94.19	0.22765	0.22329	0.22	0.27747	0.28	RANDOM	42.281

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]
0.63	0.31		0.63		-0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.705
r_scangle_it	5.62
r_scbond_it	3.822
r_mcangle_it	3.288
r_angle_refined_deg	2.929
r_mcbond_it	1.951
r_angle_other_deg	1.522
r_symmetry_vdw_refined	0.616
r_symmetry_vdw_other	0.44
r_symmetry_hbond_refined	0.436
r_nbd_other	0.277
r_nbd_refined	0.264
r_xyhbond_nbd_refined	0.196
r_chiral_restr	0.177
r_nbtor_other	0.105
r_bond_refined_d	0.043
r_gen_planes_refined	0.016
r_gen_planes_other	0.014
r_bond_other_d	0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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	2866
Nucleic Acid Atoms	321
Solvent Atoms	91
Heterogen Atoms	31

Software

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