5OL0

Structure of Leishmania infantum Silent Information Regulator 2 related protein 1 (LiSIR2rp1) in complex with acetylated p53 peptide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5295100mM Na Hepes pH7.5; 25% PEG2000 MME
Crystal Properties
Matthews coefficientSolvent content
2.0640.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.02α = 90
b = 65.67β = 97.75
c = 66.62γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.978SOLEILPROXIMA 1

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
11.9946.5698.80.04715.433.338331
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)
11.992.1195.40.5062.23.14

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 REPLACEMENTTHROUGHOUT3glt1.9946.5636411191798.780.170050.167130.22577RANDOM41.374
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]
0.251.21-1.681.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.459
r_dihedral_angle_4_deg16.351
r_dihedral_angle_3_deg14.159
r_long_range_B_refined8.697
r_long_range_B_other8.688
r_scangle_other6.81
r_dihedral_angle_1_deg5.873
r_mcangle_it4.71
r_mcangle_other4.71
r_scbond_it4.534
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.459
r_dihedral_angle_4_deg16.351
r_dihedral_angle_3_deg14.159
r_long_range_B_refined8.697
r_long_range_B_other8.688
r_scangle_other6.81
r_dihedral_angle_1_deg5.873
r_mcangle_it4.71
r_mcangle_other4.71
r_scbond_it4.534
r_scbond_other4.533
r_mcbond_it3.441
r_mcbond_other3.427
r_angle_refined_deg1.832
r_angle_other_deg1.09
r_chiral_restr0.107
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4385
Nucleic Acid Atoms
Solvent Atoms239
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MrBUMPphasing