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Crystal structure of a human Notch1 ankyrin domain mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YYH PDB ENTRY 1YYH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 0.55M Sodium/Potassium Tartrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.26 62.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.982 α = 90 b = 96.982 β = 90 c = 108.719 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 315 2006-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9769 ESRF ID14-1
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 50 99.9 0.066 0.066 10.6 10.7 45594 45547 3 26.6
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 99.9 0.488 0.488
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 1YYH 1.9 48.51 45547 43201 2297 99.9 0.18998 0.18998 0.18777 0.1877 0.23094 0.2307 RANDOM 31.288
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.112 r_dihedral_angle_4_deg 19.929 r_dihedral_angle_3_deg 13.524 r_scangle_it 5.677 r_dihedral_angle_1_deg 5.659 r_scbond_it 4.329 r_mcangle_it 3.973 r_mcbond_it 3.341 r_angle_refined_deg 1.491 r_symmetry_hbond_refined 0.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.112 r_dihedral_angle_4_deg 19.929 r_dihedral_angle_3_deg 13.524 r_scangle_it 5.677 r_dihedral_angle_1_deg 5.659 r_scbond_it 4.329 r_mcangle_it 3.973 r_mcbond_it 3.341 r_angle_refined_deg 1.491 r_symmetry_hbond_refined 0.338 r_symmetry_vdw_refined 0.325 r_nbtor_refined 0.298 r_xyhbond_nbd_refined 0.237 r_nbd_refined 0.232 r_chiral_restr 0.115 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2969 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement AMoRE phasing