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Apolipoprotein E4, 22k domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BZ4 PDB ENTRY 1BZ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 50MM NA-CACODYLATE, PH 5.6, 20-25% PEG 400, 1% 2-ME, RT, CRYSTALLIZED FROM FULL LENGTH APOE4 CONSTRUCT (299 RESIDUES). PROTEOLYTIC CLEAVAGE IN CRYSTALLIZATION DROP TO 22K FRAGMENT. NEW, THIRD ORTHOGONAL CRYSTAL FORM OF APOE (ORTHO-3)
Crystal Properties Matthews coefficient Solvent content 2.56 49.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.511 α = 90 b = 53.089 β = 90 c = 73.372 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 125 CCD ADSC CCD MIRRORS 1999-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 20.9 99.97 0.035 12.1 7.7 20168
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1BZ4 1.7 20.9 19116 1045 100 0.219 0.218 0.2196 0.247 RANDOM 30.25
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] -0.4 -1 1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.592 r_dihedral_angle_1_deg 4.161 r_scangle_it 4.111 r_scbond_it 2.507 r_mcangle_it 2.354 r_angle_refined_deg 1.794 r_mcbond_it 1.237 r_symmetry_vdw_refined 0.257 r_nbd_refined 0.232 r_symmetry_hbond_refined 0.232
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.592 r_dihedral_angle_1_deg 4.161 r_scangle_it 4.111 r_scbond_it 2.507 r_mcangle_it 2.354 r_angle_refined_deg 1.794 r_mcbond_it 1.237 r_symmetry_vdw_refined 0.257 r_nbd_refined 0.232 r_symmetry_hbond_refined 0.232 r_xyhbond_nbd_refined 0.222 r_chiral_restr 0.117 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 1179 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling EPMR phasing