Experiment: 2PFN

Na in the active site of DNA Polymerase lambda

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XSN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	278	10-20% 2-propanol, 0.2 M sodium citrate and 0.1M sodium cacodylate , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.082	α = 90
b = 61.557	β = 90
c = 140.532	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	RIGAKU SATURN 92			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	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	1.9	50	97.6	0.088	23	4.8		37287

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)
	1.9	1.97	94.3		0.587		3.4	3547

Refinement

Statistics
Diffraction ID	Structure Solution 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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1XSN	1.9	50	35075	1755	91.2	0.213	0.2146	0.232	0.2355	40.549

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]
4.628			-5.973		1.345

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.488
c_mcangle_it	2.167
c_scbond_it	1.735
c_mcbond_it	1.323

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2438
Nucleic Acid Atoms	426
Solvent Atoms	307
Heterogen Atoms	34

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing