3C4N

Crystal structure of DR_0571 protein from Deinococcus radiodurans in complex with ADP. Northeast Structural Genomics Consortium Target DrR125


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH UNDER OIL7.5277Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM DTT. Precipitant cocktail: 20% PEG 20000, 100 mM Lithium chloride, 100 mM Sodium acetate, MICROBATCH UNDER OIL, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.627α = 90
b = 67.829β = 91.14
c = 83.645γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Mirrors2007-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97918APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.43090.80.0760.105101.6654216542125.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.42.4997.50.1630.1913.641.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)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 DIFFRACTIONSADTHROUGHOUT2.419.9826542155556545077.40.2110.2110.245RANDOM28.9
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]
-0.855.42-1.172.02
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.5
c_angle_deg1.4
c_improper_angle_d0.98
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.5
c_angle_deg1.4
c_improper_angle_d0.98
c_bond_d0.007
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_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5248
Nucleic Acid Atoms
Solvent Atoms372
Heterogen Atoms54

Software

Software
Software NamePurpose
CNSrefinement
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing