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Structure of the Notch3 NRR in complex with an antibody Fab Fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XGP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 100 mM sodium Citrate pH 5.5, 12 % PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.67 53.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.652 α = 90 b = 158.951 β = 90 c = 159.687 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 170 CCD ADSC QUANTUM 210 2012-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.98 159.69 99.9 0.189 0.079 10 6.7 70289 75.47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.98 3.14 100 1.099 0.456 1.7 6.7
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 1xgp 2.98 112.66 70204 3541 99.9 0.234 0.233 0.256 0.2548 RANDOM 57.74
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] -19.2602 15.9061 3.354
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.74 t_omega_torsion 2.39 t_angle_deg 1.04 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.74 t_omega_torsion 2.39 t_angle_deg 1.04 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18838 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 69
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing