2AWA

Crystal structure of DNA polymerase III, beta chain (EC 2.7.7.7) (np_344555.1) from STREPTOCOCCUS PNEUMONIAE TIGR4 at 2.50 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	7.5	277	10.0% iso-Propanol, 20.0% PEG-4000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.06	α = 90
b = 70.72	β = 91.04
c = 135.44	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	MARMOSAIC 325 mm CCD		2005-06-02	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97934, 0.91837, 0.97923	SSRL	BL9-2

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	48.9	91.1	0.088	8			59570

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	2.6		74.4	0.678	1.85

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD, MOLECULAR REPLACEMENT	THROUGHOUT	1MMI	2.5	30	56494	3044	48.91	0.195	0.192	0.25	RANDOM	60.175

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]
-0.36		-2.72	-2.04		2.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.874
r_dihedral_angle_4_deg	16.323
r_dihedral_angle_3_deg	15.183
r_scangle_it	7.047
r_dihedral_angle_1_deg	6.467
r_scbond_it	4.657
r_mcangle_it	2.551
r_mcbond_it	1.542
r_angle_refined_deg	1.294
r_angle_other_deg	0.735
r_mcbond_other	0.291
r_symmetry_vdw_other	0.206
r_nbd_refined	0.202
r_nbtor_refined	0.174
r_nbd_other	0.173
r_xyhbond_nbd_refined	0.146
r_nbtor_other	0.083
r_chiral_restr	0.073
r_symmetry_hbond_refined	0.073
r_symmetry_vdw_refined	0.071
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11381
Nucleic Acid Atoms
Solvent Atoms	251
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing
MOLREP	phasing