3E0J | pdb_00003e0j

X-ray structure of the complex of regulatory subunits of human DNA polymerase delta

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	100 mM imidazole, pH 6.5, 450 mM sodium acetate, 5 mM tris(2-carboxyethyl)phosphine hydrochloride (TCEP), and 1%(v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.27	71.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.128	α = 90
b = 248.535	β = 106.94
c = 103.461	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	IMAGE PLATE	RIGAKU RAXIS IV	Osmic VariMaxTM HR mirror	2007-12-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

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	40	93	0.079	21.2	2.6		85645		-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)
	3	3.11	90.4		0.43	3.8	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MIR	THROUGHOUT	3	29.89	83574	4224	91.3	0.257	0.257	0.26	0.281	0.28	RANDOM	60.4

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]
1.83		5.22	-0.86		-0.96

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.8
c_mcangle_it	2.72
c_scangle_it	2.6
c_angle_deg	1.6
c_scbond_it	1.53
c_mcbond_it	1.49
c_improper_angle_d	1.08
c_bond_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17092
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
CrystalClear	data collection
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing

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.