Experiment: 2IHM

Polymerase mu in ternary complex with gapped 11mer DNA duplex and bound incoming nucleotide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JMS	murine TdT - 1JMS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.095M Na Citrate pH 5.6, 19% ispropanol, 19% PEG4000, and 5% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.028	α = 90
b = 96.085	β = 106.55
c = 73.09	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	93	CCD	MARMOSAIC 300 mm CCD	mirrors	2005-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.4	50	99.7	0.106	0.106	16.1	3.5	36847	36737		-3	45

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.4	2.49	99.5		0.505	0.505	2.5	3.5	3645

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 (All)	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	murine TdT - 1JMS	2.4	50	2	35276	35276	1653	99.7	0.232	0.232	0.23	0.2205	0.277	0.2693	random	58.5

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]
0.37		3.39	5.79		-6.16

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.1
c_angle_deg	1.3
c_improper_angle_d	1.17
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5246
Nucleic Acid Atoms	850
Solvent Atoms	183
Heterogen Atoms	61

Software

Software
Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
CNS	refinement
MAR345	data collection
HKL-2000	data reduction
SCALEPACK	data scaling