3U3D

Plasmodium falciparum Sir2A preferentially hydrolyzes medium and long chain fatty acyl lysine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3JWPPDB ENTRY 3JWP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29816% PEG 3350, 0.1M NaF, 7% Formamide, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6353.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.511α = 90
b = 103.328β = 90
c = 105.512γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102009-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A11.97CHESSA1

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
12.45098.50.1496.78.214365
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)
12.42.4497.20.7534.4689

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 3JWP2.4501428972098.020.22640.22380.2761RANDOM59.554
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]
-1.28-0.141.42
RMS Deviations
KeyRefinement Restraint Deviation
r_scbond_it52.148
r_dihedral_angle_2_deg41.389
r_scangle_it29.791
r_mcangle_it23.346
r_dihedral_angle_3_deg20.564
r_mcbond_it20.254
r_dihedral_angle_4_deg13.804
r_dihedral_angle_1_deg7.781
r_angle_refined_deg2.1
r_chiral_restr0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_scbond_it52.148
r_dihedral_angle_2_deg41.389
r_scangle_it29.791
r_mcangle_it23.346
r_dihedral_angle_3_deg20.564
r_mcbond_it20.254
r_dihedral_angle_4_deg13.804
r_dihedral_angle_1_deg7.781
r_angle_refined_deg2.1
r_chiral_restr0.13
r_bond_refined_d0.047
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2111
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms7

Software

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