1J6O

Crystal structure of TatD-related deoxyribonuclease (TM0667) from Thermotoga maritima at 1.8 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.629319 % iso-Propanol/19 % PEG 4000; 0.095 M citrate pH 5.6, 5 % Glycerol, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K, pH 5.60
Crystal Properties
Matthews coefficientSolvent content
1.7830.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.05α = 90
b = 77.25β = 90
c = 84.53γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152002-04-01MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.918370, 0.979224, 0.978932SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.829.8698.60.104178.72171711.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.8587.10.5392.65.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.829.882164821648105198.50.190.190.224RANDOM18.5
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]
0.83-1.841.02
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it3.6
c_scbond_it2.41
c_mcangle_it2.07
c_angle_deg1.77
c_mcbond_it1.41
c_bond_d0.011
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it3.6
c_scbond_it2.41
c_mcangle_it2.07
c_angle_deg1.77
c_mcbond_it1.41
c_bond_d0.011
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2097
Nucleic Acid Atoms
Solvent Atoms199
Heterogen Atoms

Software

Software
Software NamePurpose
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
CCP4data reduction
SnBphasing
MLPHAREphasing
CCP4model building
SOLVEphasing
CNSrefinement
CCP4data scaling
RESOLVEphasing