Experiment: 4P2H

Structure of human DNA polymerase complexed with N7MG in the template opposite to incoming non-hydrolyzable TTP with manganese in the active site

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	14%-23% PEG3400, 350 mM sodium acetate, 50 mM imidazole

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.767	α = 90
b = 79.167	β = 106.18
c = 54.982	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	ADSC QUANTUM 315r		2013-12-15		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.97648	ALS	5.0.3

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	1.99	20	100	0.086	7.8	5.6		30969			25.96

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	1.99	2.02	100		0.445		5.6	1552

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	1bxp	1.987	19.792	30158	1520	96.97	0.2063	0.204	0.204	0.2495	0.2494	29.25

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.519
f_angle_d	1.219
f_chiral_restr	0.076
f_bond_d	0.005
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2576
Nucleic Acid Atoms	634
Solvent Atoms	168
Heterogen Atoms	33

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
PHENIX	refinement