2W7O | pdb_00002w7o

Structure and Activity of Bypass Synthesis by Human DNA Polymerase Kappa Opposite the 7,8-Dihydro-8-oxodeoxyguanosine Adduct

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OH2	PDB ENTRY 2OH2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		175 MM NACL, 25 MM HEPES PH 7.3, 5 MM GLYCEROL, 2.5 MM 2-MERCHAPTOETHANOL, 0.5 MM TECEP, 5 MM CACL2, 5 MM DGTP, 9% PEG5000MME, 0.1 M AMMONIUM ACETATE, 10 MM MES PH 6.5

Crystal Properties
Matthews coefficient	Solvent content
4.4	74.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 165.482	α = 90
b = 217.629	β = 90
c = 117.957	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	MARRESEARCH		2007-10-20	M	SINGLE WAVELENGTH

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

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	3.16	49.41	95	0.15	11	6.8		35030			63.5

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	3.16	3.36	76.1		0.54	2.73	3.7

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 ENTRY 2OH2	3.16	49.41	35013	1751	95	0.241	0.241	0.24	0.278	0.28	RANDOM	96.7

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]
33.42			-41.41		7.98

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.7
c_scangle_it	2.92
c_mcangle_it	2.21
c_improper_angle_d	1.77
c_scbond_it	1.7
c_angle_deg	1.4
c_mcbond_it	1.24
c_bond_d	0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6904
Nucleic Acid Atoms	1136
Solvent Atoms	30
Heterogen Atoms	66

Software

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