4YFU | pdb_00004yfu

Crystal structure of open Bacillus fragment DNA polymerase bound to DNA and dTTP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	290	~50% ammonium sulfate, MES pH 5.8, magnesium sulfate, methyl pentanediol

Crystal Properties
Matthews coefficient	Solvent content
2.62	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.23	α = 90
b = 108.1	β = 90
c = 151.34	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	100	CCD	MARMOSAIC 300 mm CCD		2007-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.5	44.7	99	0.063	0.071	13.33	4.61		241163		-3	28.063

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.59	96.2		0.498	0.584	2.79	3.38

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	1.5	44.68	230017	11140	98.98	0.1966	0.195	0.195	0.2303	0.2303	RANDOM	28.759

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]
-0.05			0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.625
r_dihedral_angle_4_deg	17.606
r_dihedral_angle_3_deg	15.335
r_dihedral_angle_1_deg	6.165
r_scbond_it	4.456
r_mcangle_it	3.401
r_mcbond_it	2.674
r_angle_refined_deg	2.529
r_chiral_restr	0.166
r_bond_refined_d	0.024
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9307
Nucleic Acid Atoms	836
Solvent Atoms	1371
Heterogen Atoms	118

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
REFMAC	phasing
Coot	model building