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

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MMI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP7.527710.0% iso-Propanol, 20.0% PEG-4000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7655.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.06α = 90
b = 70.72β = 91.04
c = 135.44γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2005-06-02MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97934, 0.91837, 0.97923SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.548.991.10.088859570
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.674.40.6781.85

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMAD, MOLECULAR REPLACEMENTTHROUGHOUT1MMI2.53056494304448.910.1950.1920.25RANDOM60.175
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]
-0.36-2.72-2.042.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.874
r_dihedral_angle_4_deg16.323
r_dihedral_angle_3_deg15.183
r_scangle_it7.047
r_dihedral_angle_1_deg6.467
r_scbond_it4.657
r_mcangle_it2.551
r_mcbond_it1.542
r_angle_refined_deg1.294
r_angle_other_deg0.735
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.874
r_dihedral_angle_4_deg16.323
r_dihedral_angle_3_deg15.183
r_scangle_it7.047
r_dihedral_angle_1_deg6.467
r_scbond_it4.657
r_mcangle_it2.551
r_mcbond_it1.542
r_angle_refined_deg1.294
r_angle_other_deg0.735
r_mcbond_other0.291
r_symmetry_vdw_other0.206
r_nbd_refined0.202
r_nbtor_refined0.174
r_nbd_other0.173
r_xyhbond_nbd_refined0.146
r_nbtor_other0.083
r_chiral_restr0.073
r_symmetry_hbond_refined0.073
r_symmetry_vdw_refined0.071
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11381
Nucleic Acid Atoms
Solvent Atoms251
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
MOLREPphasing