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Crystal structure of BACE1 in complex with 2-aminooxazoline-3-azaxanthene compound 12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W50
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.6 298 21% polyethylene glycol 5000 MME, 180 mM sodium citrate (pH 6.6), 200 mM ammonium iodide, 3% (v/v) DMSO
Crystal Properties Matthews coefficient Solvent content 2.81 56.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.287 α = 90 b = 102.287 β = 90 c = 170.374 γ = 120
Symmetry Space Group P 61 2 2
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++ 2010-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 1.9 50 99.4 0.071 15.3 6.8 41991 -3
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 1.9 1.97 95 0.453 2.4 3 3935
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 1W50 1.9 50 39815 2116 99.42 0.2064 0.2052 0.2057 0.228 0.2285 RANDOM 29.7
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] -0.25 -0.13 -0.25 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.705 r_dihedral_angle_4_deg 15.198 r_dihedral_angle_3_deg 12.214 r_dihedral_angle_1_deg 6.367 r_angle_refined_deg 1.258 r_angle_other_deg 0.835 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.705 r_dihedral_angle_4_deg 15.198 r_dihedral_angle_3_deg 12.214 r_dihedral_angle_1_deg 6.367 r_angle_refined_deg 1.258 r_angle_other_deg 0.835 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2914 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 45
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction AMoRE phasing DENZO data reduction SCALEPACK data scaling