3RAQ | pdb_00003raq

Dpo4 extension ternary complex with 3'-terminal primer C base opposite the 1-methylguanine (MG1) lesion

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GIJ	PDB ENTRY 3GIJ

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 and 10% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.194	α = 98.97
b = 62.077	β = 103.82
c = 91.459	γ = 93.72

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		CCD	ADSC QUANTUM 315		2006-07-20	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	2.25	20	98.4	0.107		3.6		51859		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.31	96.8		2	2.8	3622

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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 3GIJ	2.25	20	2	51859	48438	2578	98.27	0.19589	0.19379	0.2	0.23505	0.24	RANDOM	44.889

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]
-2.05	0.06	-0.32	0.05	-0.05	1.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.672
r_dihedral_angle_4_deg	18.619
r_dihedral_angle_3_deg	14.87
r_dihedral_angle_1_deg	5.2
r_scangle_it	2.04
r_angle_refined_deg	1.42
r_scbond_it	1.259
r_angle_other_deg	0.895
r_mcangle_it	0.883
r_mcbond_it	0.523

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.672
r_dihedral_angle_4_deg	18.619
r_dihedral_angle_3_deg	14.87
r_dihedral_angle_1_deg	5.2
r_scangle_it	2.04
r_angle_refined_deg	1.42
r_scbond_it	1.259
r_angle_other_deg	0.895
r_mcangle_it	0.883
r_mcbond_it	0.523
r_chiral_restr	0.118
r_mcbond_other	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5480
Nucleic Acid Atoms	1237
Solvent Atoms	298
Heterogen Atoms	98

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.