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Human Notch1 EGF domains 11-13 mutant fucosylated at T466
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VJ3 PDB ENTRY 2VJ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.21 44.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.29 α = 90 b = 28.29 β = 90 c = 282.732 γ = 120
Symmetry Space Group P 31 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 PIXEL DECTRIS PILATUS 6M 2012-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.85 24.14 93.5 0.07 3.3 10837
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 1.85 1.9 95.3 0.42 3 5.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2VJ3 1.85 24.14 10837 540 91.94 0.22572 0.22406 0.25992 0.243 RANDOM 23.172
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] 0.01 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.396 r_dihedral_angle_4_deg 24.57 r_dihedral_angle_3_deg 11.661 r_dihedral_angle_1_deg 5.623 r_angle_refined_deg 1.112 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.215 r_symmetry_hbond_refined 0.107 r_metal_ion_refined 0.096 r_xyhbond_nbd_refined 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.396 r_dihedral_angle_4_deg 24.57 r_dihedral_angle_3_deg 11.661 r_dihedral_angle_1_deg 5.623 r_angle_refined_deg 1.112 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.215 r_symmetry_hbond_refined 0.107 r_metal_ion_refined 0.096 r_xyhbond_nbd_refined 0.082 r_chiral_restr 0.072 r_symmetry_metal_ion_refined 0.064 r_nbtor_refined 0.032 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 914 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing