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X-ray crystal structure of beta secretase complexed with compound 8c
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W50 PDB ENTRY 1W50
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 20-22.5% (W/V) PEG 5000 MONOMETHYLETHYL (MME), 200 MM SODIUM CITRATE (PH 6.6) AND 200 MM AMMONIUM IODIDE
Crystal Properties Matthews coefficient Solvent content 2.96 58.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.138 α = 90 b = 102.138 β = 90 c = 168.258 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 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 SRS PX14.1
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 2.75 50 98.8 0.12 2.4 13125
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 2.75 2.82 99.9 0.46
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 1W50 2.75 51.07 13125 690 97.9 0.232 0.228 0.2333 0.319 0.3242 RANDOM 38.27
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] 0.36 0.18 0.36 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.384 r_dihedral_angle_3_deg 17.135 r_dihedral_angle_4_deg 16.251 r_dihedral_angle_1_deg 7.472 r_angle_refined_deg 1.391 r_angle_other_deg 0.872 r_symmetry_vdw_refined 0.219 r_nbd_refined 0.214 r_nbd_other 0.202 r_symmetry_vdw_other 0.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.384 r_dihedral_angle_3_deg 17.135 r_dihedral_angle_4_deg 16.251 r_dihedral_angle_1_deg 7.472 r_angle_refined_deg 1.391 r_angle_other_deg 0.872 r_symmetry_vdw_refined 0.219 r_nbd_refined 0.214 r_nbd_other 0.202 r_symmetry_vdw_other 0.193 r_nbtor_refined 0.192 r_symmetry_hbond_refined 0.192 r_xyhbond_nbd_refined 0.188 r_nbtor_other 0.089 r_scangle_it 0.087 r_chiral_restr 0.078 r_mcangle_it 0.074 r_scbond_it 0.069 r_mcbond_it 0.047 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2966 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling CSearch phasing