3RMA | pdb_00003rma

Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	297	10-11 % PEG 2000 MME, 100 mM Na acetate, 150 mM MgSO4, 100 mM Hepes, 6-10 % glycerol, 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K, pH 7.2, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.699	α = 90
b = 123	β = 96.08
c = 163.941	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	CCD	MARMOSAIC 300 mm CCD	ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY	2008-10-23	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY	2009-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.033202	APS	23-ID-B
2	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.033202	APS	23-ID-D

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	2.84	50	99.8	0.17	10.7	7.9		125223

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	2.84	2.94	99.8		0.764	2.03	6.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	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		2.84	50	121436	22149	94.6	0.2146	0.21	0.2746	0.27	73.6554

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]
-2.987		4.273	-6.21		9.197

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.906
c_mcangle_it	2.302
c_scbond_it	1.806
c_mcbond_it	1.319
c_angle_d	1.236
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28891
Nucleic Acid Atoms	2236
Solvent Atoms	324
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	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.