☰ Navigation Tabs
X-ray Structure of the N-terminally truncated human APEP-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FHG SWISS MODEL (PDB ENTRIES 1FHG, 1BIH, 1CS6) experimental model PDB 1BIH SWISS MODEL (PDB ENTRIES 1FHG, 1BIH, 1CS6) experimental model PDB 1CS6 SWISS MODEL (PDB ENTRIES 1FHG, 1BIH, 1CS6)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 30% PEG MME 2000, 200mM (NH4)2SO4, 100mM Na Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.8 32.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.541 α = 90 b = 25.522 β = 104.59 c = 42.544 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 IMAGE PLATE MARRESEARCH mirrors 2004-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 0.96 20 89.1 0.07 0.07 29.9 3.9 183130 46733
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 0.96 0.98 47.3 0.16 0.16 4.5 1.9 1651
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 SWISS MODEL (PDB ENTRIES 1FHG, 1BIH, 1CS6) 0.96 5 43956 2384 89.67 0.16113 0.16053 0.1814 0.17213 0.1895 RANDOM 7.249
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] -0.64 -0.38 0.58 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.676 r_dihedral_angle_3_deg 13.534 r_dihedral_angle_4_deg 9.418 r_sphericity_free 8.013 r_dihedral_angle_1_deg 6.654 r_scangle_it 3.808 r_sphericity_bonded 3.157 r_angle_other_deg 3 r_scbond_it 2.94 r_mcangle_it 2.387
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.676 r_dihedral_angle_3_deg 13.534 r_dihedral_angle_4_deg 9.418 r_sphericity_free 8.013 r_dihedral_angle_1_deg 6.654 r_scangle_it 3.808 r_sphericity_bonded 3.157 r_angle_other_deg 3 r_scbond_it 2.94 r_mcangle_it 2.387 r_mcbond_it 1.917 r_angle_refined_deg 1.782 r_rigid_bond_restr 1.302 r_mcbond_other 0.671 r_symmetry_vdw_other 0.323 r_symmetry_vdw_refined 0.289 r_nbd_refined 0.217 r_nbd_other 0.217 r_symmetry_hbond_refined 0.211 r_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.174 r_chiral_restr 0.099 r_nbtor_other 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 766 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing