4RUA

Crystal structure of Y-family DNA polymerase Dpo4 bypassing a MeFapy-dG adduct

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	298	50 MM TRIS HCL,PH 7.4, 15% PEG3350, 100MM CALCIUM DIACETATE, 2.5% GLYCEROL , VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.451	α = 90
b = 102.716	β = 90
c = 53.432	γ = 90

Symmetry
Space Group	P 21 21 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	MARMOSAIC 300 mm CCD		2010-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.07810	APS	21-ID-D

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	3.068	50	98.4	0.112	0.112	16.378	6.2		10134		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.1	3.15	84.7		0.68	0.68	1.072	3.1

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 code 2BQU	3.07	50	9612	521	98.02	0.16843	0.1633	0.17	0.25827	0.25	RANDOM	88.239

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]
1.29			-0.92		-0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.216
r_dihedral_angle_3_deg	18.14
r_long_range_B_refined	15.826
r_long_range_B_other	15.826
r_dihedral_angle_4_deg	12.19
r_scangle_other	11.388
r_mcangle_it	8.542
r_mcangle_other	8.315
r_scbond_it	7.66
r_scbond_other	7.27
r_dihedral_angle_1_deg	6.949
r_mcbond_other	5.713
r_mcbond_it	5.712
r_angle_refined_deg	1.527
r_angle_other_deg	1.267
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	2744
Nucleic Acid Atoms	611
Solvent Atoms	36
Heterogen Atoms	33

Software

Software
Software Name	Purpose
MD2	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling