4G06

Crystal structure of protein SP_0782 (7-79) from Streptococcus pneumoniae complexed with ssDNA. Northeast Structural Genomics Consortium (NESG) target SPR104


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OBH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.2291Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution:0.1M (NH4)2HPO4 0.1M Na3Citrate, PEG1K 40%, 3% Ethylene Glycol, macrobatch under oil, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.9336.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.722α = 90
b = 62.722β = 90
c = 73.441γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2012-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4C0.97915NSLSX4C

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
12.94892.20.0977.71.911389-340.32

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3OBH2.90528.8410.8111389607826898.510.2080.2050.263random30.132
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]
1.5431.543-3.086
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.413
f_angle_d1.327
f_chiral_restr0.077
f_bond_d0.009
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1099
Nucleic Acid Atoms
Solvent Atoms3
Heterogen Atoms48

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing