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Crystal structure of the human Notch1 Negative Regulatory Region (NRR) bound to the fab fragment of an antagonist antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OO4 pdb 2OO4, fab fragment
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 292 Equal volumes of protein and well solutions. Protein: 6 mg/mL in 150 mM NaCl, 20 mM Bis-Tris pH 6.5. Well solution: 300 mM di-Ammonium Sulfate, 20% PEG 5000 MME, 100 mM Tris pH 7.5, VAPOR DIFFUSION, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.26 45.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.254 α = 90 b = 163.934 β = 90 c = 179.62 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 93 CCD ADSC QUANTUM 315 2008-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.000 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 2.19 30 97.4 0.098 14.9 6.6 71794 69923 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.19 2.32 88.5 0.496 4.2 5.5
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 pdb 2OO4, fab fragment 2.19 30 62930 6979 97.76 0.22721 0.22233 0.2268 0.27076 0.2722 RANDOM 27.279
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] -1.92 0.4 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.236 r_dihedral_angle_4_deg 17.149 r_dihedral_angle_3_deg 15.618 r_dihedral_angle_1_deg 5.872 r_mcangle_it 3.579 r_scangle_it 3.199 r_mcbond_it 2.397 r_scbond_it 2.202 r_angle_refined_deg 1.139 r_angle_other_deg 0.821
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.236 r_dihedral_angle_4_deg 17.149 r_dihedral_angle_3_deg 15.618 r_dihedral_angle_1_deg 5.872 r_mcangle_it 3.579 r_scangle_it 3.199 r_mcbond_it 2.397 r_scbond_it 2.202 r_angle_refined_deg 1.139 r_angle_other_deg 0.821 r_mcbond_other 0.57 r_symmetry_vdw_other 0.197 r_symmetry_vdw_refined 0.19 r_nbd_refined 0.188 r_nbd_other 0.185 r_nbtor_refined 0.174 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.14 r_metal_ion_refined 0.119 r_nbtor_other 0.082 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9986 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 39
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling