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Structure of bace (beta secretase) in complex with inhibitor
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 6 273 10% PEG 4000, 100MM MES PH 6.0, VAPOR DIFFUSION, TEMPERATURE 273K, temperature 273 KK
Crystal Properties Matthews coefficient Solvent content 2.53 51.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 229.196 α = 90 b = 98.829 β = 103.36 c = 63.132 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 SLS X06DA
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 1.8 111.8 94.7 0.053 7.2 2.2 126584
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 1.8 1.9 94.2 0.678 1 2.2
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 2B8L 1.8 111.8 118247 1212 94.37 0.1775 0.17718 0.247 0.20846 0.2661 RANDOM 16.593
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] -1.96 -0.86 -1.33 2.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.8 r_dihedral_angle_4_deg 21.997 r_dihedral_angle_3_deg 13.639 r_dihedral_angle_1_deg 6.833 r_scangle_it 5.177 r_scbond_it 3.94 r_mcangle_it 2.589 r_mcbond_it 2.134 r_angle_refined_deg 1.353 r_angle_other_deg 0.743
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.8 r_dihedral_angle_4_deg 21.997 r_dihedral_angle_3_deg 13.639 r_dihedral_angle_1_deg 6.833 r_scangle_it 5.177 r_scbond_it 3.94 r_mcangle_it 2.589 r_mcbond_it 2.134 r_angle_refined_deg 1.353 r_angle_other_deg 0.743 r_mcbond_other 0.554 r_symmetry_vdw_refined 0.318 r_symmetry_vdw_other 0.26 r_nbd_other 0.193 r_nbd_refined 0.19 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.148 r_symmetry_hbond_refined 0.131 r_nbtor_other 0.088 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8824 Nucleic Acid Atoms Solvent Atoms 646 Heterogen Atoms 147
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling