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Crystal structure of the human Notch 1 ankyrin domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OT8 PDB ENTRY 1OT8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 ammonium hydrogen phosphate, sodium chloride, imidazole, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.7 54.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.84 α = 90 b = 96.84 β = 90 c = 108.996 γ = 120
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 QUANTUM 4 2005-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 1.488 SRS PX14.1
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 1.9 83.92 98.5 0.079 0.079 12.4 3.6 44926 44926 2.5 26.9
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) 1.9 1.94 98.6 0.385 0.385 12.4 3.6 3138
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1OT8 1.901 83.92 44926 42631 2261 98.53 0.16272 0.16272 0.16112 0.1601 0.19264 0.1912 RANDOM 26.781
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] 0.72 0.36 0.72 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.899 r_dihedral_angle_4_deg 14.885 r_dihedral_angle_3_deg 12.908 r_scangle_it 5.779 r_dihedral_angle_1_deg 5.367 r_scbond_it 4.011 r_mcangle_it 3.487 r_mcbond_it 2.888 r_angle_refined_deg 1.425 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.899 r_dihedral_angle_4_deg 14.885 r_dihedral_angle_3_deg 12.908 r_scangle_it 5.779 r_dihedral_angle_1_deg 5.367 r_scbond_it 4.011 r_mcangle_it 3.487 r_mcbond_it 2.888 r_angle_refined_deg 1.425 r_nbtor_refined 0.295 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.197 r_symmetry_hbond_refined 0.195 r_symmetry_vdw_refined 0.12 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2944 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement