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Crystal structure of Bcl-xL in complex with a Quinazoline sulfonamide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YXJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 1.1M Sodium Citrate, 0.1M Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.58 52.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.598 α = 90 b = 74.484 β = 90 c = 87.828 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 IMAGE PLATE RIGAKU RAXIS IV++ Capillary 2007-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.02 50 96.45 0.072 22.9 6.2 28962 27934 -3 -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) 2.02 2.09 55.8 0.499 3.15 2525
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2YXJ 2.02 43.9 27379 26408 1450 96.45 0.19384 0.19384 0.19184 0.1931 0.23093 0.2315 RANDOM 28.758
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] -0.59 1.68 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.532 r_dihedral_angle_4_deg 16.838 r_dihedral_angle_3_deg 15.603 r_dihedral_angle_1_deg 5 r_scangle_it 2.391 r_scbond_it 1.461 r_angle_refined_deg 1.152 r_mcangle_it 1.078 r_mcbond_it 0.62 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.532 r_dihedral_angle_4_deg 16.838 r_dihedral_angle_3_deg 15.603 r_dihedral_angle_1_deg 5 r_scangle_it 2.391 r_scbond_it 1.461 r_angle_refined_deg 1.152 r_mcangle_it 1.078 r_mcbond_it 0.62 r_nbtor_refined 0.308 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.142 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2293 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 123
Software Software Software Name Purpose CrystalClear data collection PHASES phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling