3FZI

1.9 Angstrom structure of the thermophilic exonuclease III homologue Mth0212


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293reservoir: 20 % PEG 1500, 100mM HEPES pH 7.5; protein solution: 600mM NaCl, 20mM HEPES-KOH pH 7.6, 2mM DTT, vapor diffusion, sitting drop, temperature 293K
Crystal Properties
Matthew coefficientSolvent content
2.3347.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.04α = 90
b = 56.04β = 90
c = 161.32γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.80150EMBL/DESY, HamburgX13

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
11.95099.80.05836.327.522592
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)
1.91.971000.5587.32218

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1DE91.948.5122502115199.750.200810.197550.26161RANDOM28.644
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]
1.450.721.45-2.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.163
r_dihedral_angle_3_deg17.492
r_dihedral_angle_4_deg17.457
r_dihedral_angle_1_deg7.115
r_scangle_it3.226
r_scbond_it2.228
r_mcangle_it1.649
r_angle_refined_deg1.563
r_mcbond_it0.993
r_nbtor_refined0.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.163
r_dihedral_angle_3_deg17.492
r_dihedral_angle_4_deg17.457
r_dihedral_angle_1_deg7.115
r_scangle_it3.226
r_scbond_it2.228
r_mcangle_it1.649
r_angle_refined_deg1.563
r_mcbond_it0.993
r_nbtor_refined0.321
r_nbd_refined0.215
r_symmetry_vdw_refined0.17
r_xyhbond_nbd_refined0.169
r_symmetry_hbond_refined0.159
r_chiral_restr0.11
r_bond_refined_d0.015
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2152
Nucleic Acid Atoms
Solvent Atoms292
Heterogen Atoms1

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling