1Q8I | pdb_00001q8i

Crystal structure of ESCHERICHIA coli DNA Polymerase II

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.3	295	Citrate , PEG3K, DTT, EDTA, Glycerol, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
2	VAPOR DIFFUSION, HANGING DROP	5.5	295	Citrate , PEG3K, DTT, EDTA, Glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
3	VAPOR DIFFUSION, HANGING DROP	5.8	295	Citrate , PEG3K, DTT, MgCl2, Glycerol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.383	α = 90
b = 116.596	β = 90
c = 82.43	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	100	CCD	MARRESEARCH			M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	CUSTOM-MADE			M	SINGLE WAVELENGTH
3	1	x-ray						M
1,2,3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	1.0	APS	5ID-B
2	SYNCHROTRON	APS BEAMLINE 5ID-B	1.0	APS	5ID-B
3	SYNCHROTRON	APS BEAMLINE 19-ID	1.77	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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
1,2,3	2	29.7					60657

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	MIRAS	THROUGHOUT	2	20	57543	3064	99.76	0.19872	0.19672	0.2	0.23612	0.24	RANDOM	26.269

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]
-1.59			-0.64		2.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.633
r_dihedral_angle_3_deg	18.472
r_scangle_it	8.99
r_scbond_it	6.473
r_dihedral_angle_1_deg	4.816
r_mcangle_it	4.285
r_mcbond_it	3.171
r_angle_refined_deg	1.636
r_symmetry_hbond_refined	0.283
r_nbd_refined	0.24
r_symmetry_vdw_refined	0.239
r_xyhbond_nbd_refined	0.204
r_chiral_restr	0.151
r_bond_refined_d	0.017
r_gen_planes_refined	0.013
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5709
Nucleic Acid Atoms
Solvent Atoms	416
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing