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Crystal structure of a computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 PEG8000, magnesium chloride,
TrisHCl
Crystal Properties Matthews coefficient Solvent content 2.67 52.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.103 α = 90 b = 113.869 β = 90.03 c = 55.67 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2013-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.987 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.8 39.8 97.6 0.099 14.9 5.8 46840 2
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 2.07 80.1 0.249 4.47 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.8 39.8 46840 2487 82.51 0.14676 0.14502 0.17845 0.2111 RANDOM 18.168
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] -8.77 -3.76 8.02 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.264 r_dihedral_angle_4_deg 17.335 r_dihedral_angle_3_deg 16.924 r_long_range_B_refined 5.604 r_long_range_B_other 5.604 r_dihedral_angle_1_deg 5.426 r_scangle_other 3.913 r_mcangle_it 2.502 r_mcangle_other 2.502 r_scbond_it 2.441
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.264 r_dihedral_angle_4_deg 17.335 r_dihedral_angle_3_deg 16.924 r_long_range_B_refined 5.604 r_long_range_B_other 5.604 r_dihedral_angle_1_deg 5.426 r_scangle_other 3.913 r_mcangle_it 2.502 r_mcangle_other 2.502 r_scbond_it 2.441 r_scbond_other 2.438 r_angle_refined_deg 1.857 r_mcbond_it 1.636 r_mcbond_other 1.635 r_angle_other_deg 1.34 r_chiral_restr 0.123 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.005 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 Atoms Number Protein Atoms 4473 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement