3KHR | pdb_00003khr

Dpo4 post-extension ternary complex with the correct C 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
2.59	52.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.477	α = 81.76
b = 53.019	β = 76.76
c = 99.858	γ = 70.14

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		2007-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97914	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	20	96.7	0.075	15.9	4		63173		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	2.05	96.3		0.469	3.3	4	4779

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	2.01	20	59976	3185	95.9	0.20822	0.20619	0.21	0.2465	0.25	RANDOM	33.588

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]
0.4	0.81	-0.54	-1.31	1.28	0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.852
r_dihedral_angle_4_deg	17.692
r_dihedral_angle_3_deg	15.979
r_dihedral_angle_1_deg	4.913
r_scangle_it	2.821
r_scbond_it	1.743
r_angle_refined_deg	1.444
r_mcangle_it	1.296
r_mcbond_it	0.802
r_chiral_restr	0.101

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.852
r_dihedral_angle_4_deg	17.692
r_dihedral_angle_3_deg	15.979
r_dihedral_angle_1_deg	4.913
r_scangle_it	2.821
r_scbond_it	1.743
r_angle_refined_deg	1.444
r_mcangle_it	1.296
r_mcbond_it	0.802
r_chiral_restr	0.101
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5480
Nucleic Acid Atoms	1233
Solvent Atoms	402
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.