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Apo Structure of BACE (Beta Secretase)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FKN PDB ENTRY 1FKN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.6 pH 6.60
Crystal Properties Matthews coefficient Solvent content 2.86 56.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.243 α = 90 b = 103.243 β = 90 c = 169.108 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 ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.75 39.5 95.9 0.1 4.6 6.3 51594
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 1.75 1.84 97.2 0.45 1.7
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 1FKN 1.75 39.52 48964 2624 95.1 0.245 0.244 0.2483 0.283 0.2883 RANDOM 30.01
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] -0.53 -0.26 -0.53 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.215 r_scangle_it 5.221 r_mcangle_it 4.075 r_scbond_it 3.752 r_mcbond_it 2.943 r_angle_refined_deg 1.427 r_angle_other_deg 0.84 r_symmetry_vdw_other 0.29 r_nbd_other 0.24 r_symmetry_vdw_refined 0.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.215 r_scangle_it 5.221 r_mcangle_it 4.075 r_scbond_it 3.752 r_mcbond_it 2.943 r_angle_refined_deg 1.427 r_angle_other_deg 0.84 r_symmetry_vdw_other 0.29 r_nbd_other 0.24 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.218 r_symmetry_hbond_refined 0.181 r_nbtor_other 0.086 r_chiral_restr 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 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_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 279 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling EPMR phasing