5L1I

Crystal Structure of Human DNA Polymerase Eta Inserting dCTP Opposite O6-Methyl-2'-deoxyguanosine

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4O3N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	291	0.1 M MES pH 5.5, 5mM Calcium chloride, 15% PEG 2000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.095	α = 90
b = 99.095	β = 90
c = 81.869	γ = 120

Symmetry
Space Group	P 61

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	MARMOSAIC 300 mm CCD		2014-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.78	50	99.9	0.169	0.169	10.647	5.5		11577		-3

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	2.78	2.84	99.8		0.966	1.579	5.2

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	4O3N	2.78	50	10962	594	99.91	0.16353	0.15994	0.22835	RANDOM	49.131

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]
-0.12	-0.06		-0.12		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.649
r_dihedral_angle_4_deg	19.129
r_dihedral_angle_3_deg	16.267
r_long_range_B_refined	8.01
r_long_range_B_other	7.994
r_dihedral_angle_1_deg	6.775
r_scangle_other	5
r_mcangle_it	4.847
r_mcangle_other	4.846
r_scbond_it	3.096
r_scbond_other	3.093
r_mcbond_it	2.948
r_mcbond_other	2.948
r_angle_refined_deg	1.523
r_angle_other_deg	1.038
r_chiral_restr	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3366
Nucleic Acid Atoms	409
Solvent Atoms	138
Heterogen Atoms	42

Software

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