3KHL

Dpo4 post-extension ternary complex with misinserted A opposite the 2-aminofluorene-guanine [AF]G lesion

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	100 mM HEPES pH 7.0, 100 mM Calcium acetate, 10% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.389	α = 82.19
b = 52.674	β = 76.4
c = 100.103	γ = 70.07

Symmetry
Space Group	P 1

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 315		2007-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97949	APS	24-ID-C

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	2.1	20	97.6	0.047	21.2	4		55384		2

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	2.1	2.15	97.1		0.402	3.4	3.9	3947

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	PDB entry 2ASD	2.1	20	52487	2797	97.16	0.20811	0.20524	0.26254	RANDOM	33.655

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]
-0.58	1.67	-0.75	-1.07	0.63	0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.151
r_dihedral_angle_4_deg	17.545
r_dihedral_angle_3_deg	17.21
r_dihedral_angle_1_deg	5.38
r_scangle_it	2.832
r_scbond_it	1.789
r_angle_refined_deg	1.461
r_mcangle_it	1.306
r_mcbond_it	0.836
r_chiral_restr	0.104

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.151
r_dihedral_angle_4_deg	17.545
r_dihedral_angle_3_deg	17.21
r_dihedral_angle_1_deg	5.38
r_scangle_it	2.832
r_scbond_it	1.789
r_angle_refined_deg	1.461
r_mcangle_it	1.306
r_mcbond_it	0.836
r_chiral_restr	0.104
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5480
Nucleic Acid Atoms	1227
Solvent Atoms	316
Heterogen Atoms	92

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.