2HQA | pdb_00002hqa

Crystal structure of the catalytic alpha subunit of E. Coli replicative DNA polymerase III

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	18% PEG3350 0.3M NAH2PO4 0.1M HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.112	α = 90
b = 98.264	β = 90
c = 139.475	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	ADSC QUANTUM 210	Mirrors (Si111)	2005-07-15	M	SINGLE WAVELENGTH
2	1
3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1159	ALS	8.3.1

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	2.5	40	96.6	0.079	13.2	3.8		38487	1.13	1.13

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	2.5	2.59	87.9		0.792	1.13	2.8	3463

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	SAD	THROUGHOUT	2.6	20	35825	34532	1736	96.67	0.223	0.223	0.219	0.2152	0.287	0.2812	RANDOM	64.477

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]
-4.56			3.09		1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.732
r_dihedral_angle_3_deg	22.317
r_dihedral_angle_4_deg	19.87
r_dihedral_angle_1_deg	6.585
r_scangle_it	2.394
r_scbond_it	1.552
r_angle_refined_deg	1.453
r_mcangle_it	0.924
r_mcbond_it	0.615
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.732
r_dihedral_angle_3_deg	22.317
r_dihedral_angle_4_deg	19.87
r_dihedral_angle_1_deg	6.585
r_scangle_it	2.394
r_scbond_it	1.552
r_angle_refined_deg	1.453
r_mcangle_it	0.924
r_mcbond_it	0.615
r_nbtor_refined	0.315
r_symmetry_hbond_refined	0.283
r_nbd_refined	0.24
r_symmetry_vdw_refined	0.17
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.102
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7148
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	15

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.