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Crystal Structure Analysis of full-length Bcl-XL in complex with the inhibitor ABT-263
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R2D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% (w/v) PEG 3350, 0.2 M Calcium Chloride, pH approx. 7.8, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.66 25.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.14 α = 72.94 b = 85.81 β = 67.42 c = 93.64 γ = 69.38
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PILATUS 6M 2012-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.06997 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.3 47.036 97.4 0.104 6.89 89549 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 92.7 0.54 1.39
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1r2d 2.3 85 85104 4444 97.55 0.20851 0.20623 0.2112 0.25286 0.2584 RANDOM 53.066
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] -0.45 -0.27 -1.14 -0.17 1.21 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.765 r_dihedral_angle_4_deg 18.578 r_dihedral_angle_3_deg 16.979 r_mcangle_it 6.372 r_dihedral_angle_1_deg 5.795 r_scbond_it 5.237 r_mcbond_it 4.178 r_mcbond_other 4.176 r_angle_refined_deg 1.847 r_angle_other_deg 0.838
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.765 r_dihedral_angle_4_deg 18.578 r_dihedral_angle_3_deg 16.979 r_mcangle_it 6.372 r_dihedral_angle_1_deg 5.795 r_scbond_it 5.237 r_mcbond_it 4.178 r_mcbond_other 4.176 r_angle_refined_deg 1.847 r_angle_other_deg 0.838 r_chiral_restr 0.08 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14043 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 780
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction DA+ data collection XDS data reduction PHASER phasing