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Structure of EC12 Y1392W variant of BT-R1 from Manduca sexta, a Cry1A toxin binding domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EE0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.1M Tris-HCl pH 7.0, 2.8M Magnesium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.1 41.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.133 α = 90 b = 44.579 β = 107.156 c = 94.797 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 X 16M 2020-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979110 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.9 56.5 99.4 0.07 0.078 0.032 0.998 9.9 5.5 37385 -3 -3 36.2
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 1.9 1.94 99.9 0.837 0.922 0.382 0.804 1.7 5.6
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2ee0 1.9 56.5 37362 1926 99.309 0.212 0.2105 0.2194 0.2399 0.2474 Random selection 44.391
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] 2.962 -0.171 -0.051 -2.356
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.513 r_dihedral_angle_4_deg 23.572 r_dihedral_angle_3_deg 14.258 r_lrange_it 7.538 r_lrange_other 7.491 r_dihedral_angle_1_deg 7.383 r_scangle_it 4.533 r_scangle_other 4.532 r_mcangle_it 3.33 r_mcangle_other 3.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.513 r_dihedral_angle_4_deg 23.572 r_dihedral_angle_3_deg 14.258 r_lrange_it 7.538 r_lrange_other 7.491 r_dihedral_angle_1_deg 7.383 r_scangle_it 4.533 r_scangle_other 4.532 r_mcangle_it 3.33 r_mcangle_other 3.33 r_scbond_it 2.993 r_scbond_other 2.992 r_mcbond_it 2.259 r_mcbond_other 2.249 r_angle_refined_deg 1.765 r_angle_other_deg 1.437 r_symmetry_nbd_refined 0.285 r_symmetry_xyhbond_nbd_refined 0.274 r_nbd_other 0.252 r_nbd_refined 0.209 r_symmetry_nbd_other 0.199 r_xyhbond_nbd_refined 0.193 r_symmetry_xyhbond_nbd_other 0.182 r_metal_ion_refined 0.164 r_nbtor_refined 0.161 r_ncsr_local_group_1 0.116 r_ncsr_local_group_5 0.111 r_ncsr_local_group_4 0.103 r_ncsr_local_group_2 0.101 r_ncsr_local_group_3 0.097 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.077 r_ncsr_local_group_6 0.071 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3348 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing