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Tetanus neurotoxin receptor binding domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AF9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M Bis-Tris pH 6.0, 0.1 M Pottasium chloride 22.5% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.3 46.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.705 α = 90 b = 79.387 β = 90 c = 89.753 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 100 PIXEL DECTRIS EIGER X 16M 2016-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.987 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.5 50 97.6 0.073 0.079 0.03 26.9 6.7 75134
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 89.4 0.497 0.562 0.255 0.795 2.43 4.6
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 (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 1AF9 1.5 44.41 71315 3750 97.56 0.122 0.122 0.122 0.1243 0.163 0.1652 Random 24.12
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.958 r_dihedral_angle_4_deg 20.321 r_dihedral_angle_3_deg 13.528 r_dihedral_angle_1_deg 6.97 r_lrange_it 5.045 r_scangle_it 4.705 r_scbond_it 3.709 r_rigid_bond_restr 3.463 r_mcangle_it 3.266 r_mcbond_it 2.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.958 r_dihedral_angle_4_deg 20.321 r_dihedral_angle_3_deg 13.528 r_dihedral_angle_1_deg 6.97 r_lrange_it 5.045 r_scangle_it 4.705 r_scbond_it 3.709 r_rigid_bond_restr 3.463 r_mcangle_it 3.266 r_mcbond_it 2.65 r_angle_refined_deg 1.436 r_nbtor_refined 0.319 r_metal_ion_refined 0.292 r_symmetry_nbd_refined 0.268 r_symmetry_xyhbond_nbd_refined 0.232 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.106 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3565 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction pointless data scaling MOLREP phasing