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Structure of the apoptotic protease-activating factor 1 bound to ADP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.1 276 HEPES, ammonium acetate, PEG-3350, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 276K, pH 7.10
Crystal Properties Matthews coefficient Solvent content 2.4 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.955 α = 62.96 b = 92.883 β = 89.99 c = 94.988 γ = 90.05
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 4 2004-07-01 M SINGLE WAVELENGTH 2 1 x-ray M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 CHESS A1 2 SYNCHROTRON CHESS BEAMLINE A1 1.0088, 0.9500, 1.0053 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1,2 2.2 50 89.5 0.048 0.048 12.7 1.7 103300
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.21 2.27 48.9 0.267 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.21 15 102933 97722 5211 89.2 0.192 0.189 0.244 RANDOM 36.38
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] 0.18 0.13 0.77 0.4 -0.45 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.382 r_dihedral_angle_4_deg 22.503 r_dihedral_angle_3_deg 16.481 r_scangle_it 6.432 r_dihedral_angle_1_deg 6.191 r_scbond_it 4.687 r_mcangle_it 2.682 r_mcbond_it 2.19 r_angle_refined_deg 1.431 r_angle_other_deg 0.872
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.382 r_dihedral_angle_4_deg 22.503 r_dihedral_angle_3_deg 16.481 r_scangle_it 6.432 r_dihedral_angle_1_deg 6.191 r_scbond_it 4.687 r_mcangle_it 2.682 r_mcbond_it 2.19 r_angle_refined_deg 1.431 r_angle_other_deg 0.872 r_symmetry_hbond_refined 0.306 r_symmetry_vdw_refined 0.277 r_symmetry_vdw_other 0.261 r_mcbond_other 0.239 r_xyhbond_nbd_other 0.23 r_xyhbond_nbd_refined 0.213 r_nbd_refined 0.209 r_nbd_other 0.181 r_nbtor_refined 0.175 r_nbtor_other 0.088 r_chiral_restr 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18752 Nucleic Acid Atoms Solvent Atoms 803 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing