5C83

Fragment-Based Drug Discovery Targeting Inhibitor of Apoptosis Proteins: Compound 21


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OPY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52770.1M Hepes-NaOH 7.5, 3.9M NaCl

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.145α = 90
b = 71.145β = 90
c = 106.403γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442010-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54

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
12.342.6980.042.32.412242
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)
12.32.4298.50.2832.8

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 REPLACEMENTTHROUGHOUT2OPY2.3342.61112664696.10.21260.209230.27295RANDOM44.985
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]
0.220.22-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.387
r_dihedral_angle_3_deg17.359
r_dihedral_angle_4_deg14.062
r_long_range_B_refined7.573
r_dihedral_angle_1_deg5.442
r_scbond_it3.332
r_scbond_other3.329
r_mcbond_it2.418
r_angle_refined_deg1.379
r_angle_other_deg0.187
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.387
r_dihedral_angle_3_deg17.359
r_dihedral_angle_4_deg14.062
r_long_range_B_refined7.573
r_dihedral_angle_1_deg5.442
r_scbond_it3.332
r_scbond_other3.329
r_mcbond_it2.418
r_angle_refined_deg1.379
r_angle_other_deg0.187
r_chiral_restr0.113
r_bond_refined_d0.01
r_bond_other_d0.003
r_gen_planes_refined0.001
r_gen_planes_other
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_mcbond_other
r_mcangle_it
r_mcangle_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms874
Nucleic Acid Atoms
Solvent Atoms143
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing