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Structure of bace (beta secretase) in Complex with EV0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B8L PDB ENTRY 2B8L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 293 10% PEG 4000, 100mM MES pH 6.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.67 53.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 232.55 α = 90 b = 100.13 β = 103.73 c = 64.78 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 CCD MARMOSAIC 225 mm CCD 2008-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000 SLS X06DA
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 2.25 48.34 97.2 0.045 0.045 13.26 3 66620 66428 2 2 29.654
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.44 89.9 0.347 0.347 2.65 2.3 13253
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 2B8L 2.26 48.34 2 2 66620 63110 3318 100 0.22456 0.22245 0.2884 0.26487 0.3139 RANDOM 29.654
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] -5.87 -1.19 -1.46 6.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.067 r_dihedral_angle_4_deg 19.241 r_dihedral_angle_3_deg 14.154 r_dihedral_angle_1_deg 6.725 r_scangle_it 1.734 r_scbond_it 1.221 r_angle_refined_deg 1.154 r_mcangle_it 0.918 r_angle_other_deg 0.732 r_mcbond_it 0.719
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.067 r_dihedral_angle_4_deg 19.241 r_dihedral_angle_3_deg 14.154 r_dihedral_angle_1_deg 6.725 r_scangle_it 1.734 r_scbond_it 1.221 r_angle_refined_deg 1.154 r_mcangle_it 0.918 r_angle_other_deg 0.732 r_mcbond_it 0.719 r_symmetry_vdw_refined 0.269 r_symmetry_vdw_other 0.209 r_nbd_refined 0.181 r_nbtor_refined 0.178 r_nbd_other 0.169 r_xyhbond_nbd_refined 0.154 r_mcbond_other 0.118 r_xyhbond_nbd_other 0.117 r_symmetry_hbond_refined 0.102 r_nbtor_other 0.08 r_chiral_restr 0.068 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8830 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 39
Software Software Software Name Purpose SLSPX data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling