Experiment: 3D1E

Crystal structure of E. coli sliding clamp (beta) bound to a polymerase II peptide

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.2	295	27.5% PEG400, 100 mM MES pH 6.2, 100 mM calcium chloride and 1% DMSO, VAPOR DIFFUSION, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.139	α = 112.89
b = 69.869	β = 91.08
c = 73.119	γ = 99.28

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 4	mirror		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.959	NSLS	X4A

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	1.78	50	94.3	0.058	11.3		68885	60707

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2POL	1.9	33.55	52670	2646	92.9	0.226	0.2326	0.261	0.2401	random	34.929

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]
6.61	7.85	-2.78	-1.53	-1.4	-5.09

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25
c_angle_deg	1.253
c_improper_angle_d	0.78
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5733
Nucleic Acid Atoms
Solvent Atoms	472
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
CNS	phasing