3KHH | pdb_00003khh

Dpo4 extension ternary complex with a C base 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
2.69	54.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.746	α = 90
b = 98.799	β = 99.08
c = 98.638	γ = 90

Symmetry
Space Group	P 1 21 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		2007-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97918	APS	24-ID-E

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	2.7	20	98.3	0.088	13.6	3.4		27915		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	2.7	2.78	97.9		0.421	2.4	3.2	2322

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 2ASD	2.7	20	26483	1415	97.81	0.19465	0.19151	0.19	0.25239	0.26	RANDOM	28.599

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]
-0.5		-0.05	0.52		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.789
r_dihedral_angle_4_deg	18.216
r_dihedral_angle_3_deg	18.198
r_dihedral_angle_1_deg	5.355
r_scangle_it	2.032
r_angle_refined_deg	1.365
r_scbond_it	1.176
r_mcangle_it	0.85
r_mcbond_it	0.496
r_chiral_restr	0.096

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.789
r_dihedral_angle_4_deg	18.216
r_dihedral_angle_3_deg	18.198
r_dihedral_angle_1_deg	5.355
r_scangle_it	2.032
r_angle_refined_deg	1.365
r_scbond_it	1.176
r_mcangle_it	0.85
r_mcbond_it	0.496
r_chiral_restr	0.096
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5480
Nucleic Acid Atoms	1194
Solvent Atoms	92
Heterogen Atoms	96

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.