☰ Navigation Tabs
Crystal structure of SGBPdex (BT3088) with truncated residues 1-147
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold phenix.process_predicted_model to split by domain and run two simultaneous MR searches
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 MPD 1k 3350 35.5% w/v
200mM amino acid stock
100mM System 2 buffer (0.1M HEPES sodium salt and 0.1M MOPS at pH 7.5) pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.2 44.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.321 α = 90 b = 37.549 β = 100.345 c = 65.616 γ = 90
Symmetry Space Group C 1 2 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 XE 16M 2021-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.89842 Diamond I03
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 1.7 36.48 100 0.088 0.103 0.054 0.998 8 6.8 39600
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) 1.7 1.73 100 2.063 2.424 1.264 0.713 0.7 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.7 36.477 39575 2011 99.929 0.202 0.1982 0.1983 0.27 0.2702 43.417
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] -3.752 1.644 0.982 2.034
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 29.705 r_lrange_other 28.988 r_dihedral_angle_2_deg 21.183 r_dihedral_angle_3_deg 15.477 r_dihedral_angle_6_deg 14.571 r_scangle_it 8.555 r_scangle_other 8.553 r_dihedral_angle_1_deg 7.768 r_scbond_it 6.232 r_scbond_other 6.23
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 29.705 r_lrange_other 28.988 r_dihedral_angle_2_deg 21.183 r_dihedral_angle_3_deg 15.477 r_dihedral_angle_6_deg 14.571 r_scangle_it 8.555 r_scangle_other 8.553 r_dihedral_angle_1_deg 7.768 r_scbond_it 6.232 r_scbond_other 6.23 r_mcangle_other 6.031 r_mcangle_it 6.029 r_mcbond_it 4.876 r_mcbond_other 4.868 r_angle_refined_deg 2.214 r_angle_other_deg 0.899 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.188 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.149 r_nbd_other 0.143 r_symmetry_nbd_refined 0.139 r_chiral_restr 0.116 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_other 0.068 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2745 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data scaling Coot model building PHENIX phasing PHASER phasing