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The X-ray Structure of a Bak Homodimer Reveals an Inhibitory Zinc Binding Site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IMS PDB Entry 2IMS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 PEG 3350 15-30% and 0.2 M ammonium fluoride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.11 41.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.247 α = 90 b = 53.646 β = 114.87 c = 58.074 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE RIGAKU RAXIS IV Osmic multilayer confocal optics 2005-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.48 50 0.041 0.041 14.7 3.34 21001 2 1
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 1.48 1.54 0.271 2.7 1.83
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 PDB Entry 2IMS 1.49 37.32 19922 1074 79.47 0.19393 0.1925 0.1976 0.2201 0.2257 RANDOM 23.377
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] 0.2 -0.06 0.21 -0.46
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.787 r_dihedral_angle_1_deg 5.069 r_scbond_it 3.555 r_mcangle_it 2.217 r_angle_refined_deg 1.95 r_mcbond_it 1.262 r_angle_other_deg 1.038 r_symmetry_hbond_refined 0.489 r_symmetry_vdw_other 0.276 r_nbd_other 0.254
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.787 r_dihedral_angle_1_deg 5.069 r_scbond_it 3.555 r_mcangle_it 2.217 r_angle_refined_deg 1.95 r_mcbond_it 1.262 r_angle_other_deg 1.038 r_symmetry_hbond_refined 0.489 r_symmetry_vdw_other 0.276 r_nbd_other 0.254 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.227 r_symmetry_vdw_refined 0.206 r_chiral_restr 0.127 r_nbtor_other 0.095 r_metal_ion_refined 0.033 r_bond_refined_d 0.027 r_gen_planes_refined 0.012 r_gen_planes_other 0.011 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1301 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction d*TREK data scaling MOLREP phasing