2V4Q | pdb_00002v4q

Post-insertion complex of the Y-family DNA polymerase Dpo4 with M1dG containing template DNA

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.4		7.5% POLYETHYLENE GLYCOL 3350, 100 MM CALCIUM ACETATE, 25 MM TRIS HCL (PH 7.4), 100 MM SODIUM CHLORIDE, 2.5% GLYCEROL, 1 MM DGTP, 5 MM CALCIUM CHLORIDE.

Crystal Properties
Matthews coefficient	Solvent content
3.1	59.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.61	α = 90
b = 103.14	β = 90
c = 52.01	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	MARRESEARCH	MIRRORS	2008-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F		APS	21-ID-F

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	2.6	30	99	0.05	23	5.5		15832			61.8

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	2.6	2.69	96.8		0.46	4.4	5.5

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2BQR	2.6	28.72	15831	771	99.5	0.205	0.205	0.2	0.254	0.25	RANDOM	59.3

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]
-0.01			-0.25		0.26

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.6
c_scangle_it	3.05
c_mcangle_it	2.14
c_improper_angle_d	1.92
c_scbond_it	1.88
c_mcbond_it	1.25
c_angle_deg	1.2
c_bond_d	0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2744
Nucleic Acid Atoms	630
Solvent Atoms	86
Heterogen Atoms	34

Software

Software
Software Name	Purpose
CNS	refinement
XDS	data reduction
SCALEPACK	data scaling
MOLREP	phasing