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Crystal Structure of the Neurotrophin-3 and p75NTR Symmetrical Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NT3 PDB ENTRY 1NT3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 5 290 0.9M Lithium Sulfate, 0.05M Na Citrate, 0.7M Ammonium Sulfate, pH 5.0, EVAPORATION, temperature 290K
Crystal Properties Matthews coefficient Solvent content 3.18 61.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.8 α = 90 b = 125.8 β = 90 c = 133.1 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 113 CCD MAR CCD 165 mm 2007-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 1.0030 EMBL/DESY, HAMBURG BW7A
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 2.6 50 96.2 0.06 4 23326 42
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 2.6 2.66 97.3 0.381 3
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 1NT3 2.6 50 22069 22069 1190 96.18 0.22749 0.22749 0.22422 0.2226 0.28771 0.2839 RANDOM 45.243
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] 0.98 0.49 0.98 -1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.964 r_dihedral_angle_4_deg 22.814 r_dihedral_angle_3_deg 22.348 r_dihedral_angle_1_deg 8.952 r_scangle_it 2.942 r_mcangle_it 2.617 r_scbond_it 2.053 r_angle_refined_deg 1.725 r_mcbond_it 1.473 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.964 r_dihedral_angle_4_deg 22.814 r_dihedral_angle_3_deg 22.348 r_dihedral_angle_1_deg 8.952 r_scangle_it 2.942 r_mcangle_it 2.617 r_scbond_it 2.053 r_angle_refined_deg 1.725 r_mcbond_it 1.473 r_nbtor_refined 0.314 r_nbd_refined 0.25 r_symmetry_vdw_refined 0.242 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.128 r_symmetry_hbond_refined 0.076 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 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_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4080 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing