3CM2

Crystal Structure of XIAP BIR3 domain in complex with a Smac-mimetic compound, Smac010


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.529312% PEG 10K, 10% glycerol, 0.1M NaCl, pH 8.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.2261.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.529α = 90
b = 108.349β = 90
c = 225.308γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.931ESRFID14-1

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
12.54099.90.135146.56653266464
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)
2.599.90.5842.86.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3CLX2.54063088337699.940.223060.223060.220850.26379RANDOM51.255
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]
3.20.2-3.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.738
r_dihedral_angle_3_deg19.312
r_dihedral_angle_4_deg16.003
r_dihedral_angle_1_deg6.405
r_scangle_it6.166
r_scbond_it4.071
r_mcangle_it3.166
r_mcbond_it1.722
r_angle_refined_deg1.281
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.738
r_dihedral_angle_3_deg19.312
r_dihedral_angle_4_deg16.003
r_dihedral_angle_1_deg6.405
r_scangle_it6.166
r_scbond_it4.071
r_mcangle_it3.166
r_mcbond_it1.722
r_angle_refined_deg1.281
r_nbtor_refined0.31
r_nbd_refined0.211
r_chiral_restr0.21
r_symmetry_vdw_refined0.196
r_symmetry_hbond_refined0.182
r_xyhbond_nbd_refined0.114
r_metal_ion_refined0.01
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8344
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms370

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing