☰ Navigation Tabs
Dehydratase domain (PksJ DH1) from the bacillaene trans-AT PKS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 22% PEG 3350 and 0.3 M sodium formate
Crystal Properties Matthews coefficient Solvent content 1.99 38.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.905 α = 90 b = 84.79 β = 90 c = 131.938 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 2022-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 49.104 99.95 0.998 10.09 13.3 47606 27.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 0.975
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 1.9 49.104 47606 2247 99.977 0.178 0.1761 0.1864 0.2163 0.224 32.718
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] 1.916 -1.625 -0.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.973 r_dihedral_angle_3_deg 13.721 r_lrange_it 8.626 r_lrange_other 8.594 r_dihedral_angle_1_deg 7.021 r_scangle_it 6.542 r_scangle_other 6.541 r_dihedral_angle_2_deg 6.368 r_mcangle_it 4.881 r_mcangle_other 4.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.973 r_dihedral_angle_3_deg 13.721 r_lrange_it 8.626 r_lrange_other 8.594 r_dihedral_angle_1_deg 7.021 r_scangle_it 6.542 r_scangle_other 6.541 r_dihedral_angle_2_deg 6.368 r_mcangle_it 4.881 r_mcangle_other 4.88 r_scbond_it 4.11 r_scbond_other 4.109 r_mcbond_other 3.237 r_mcbond_it 3.236 r_angle_refined_deg 1.361 r_angle_other_deg 0.468 r_nbd_other 0.255 r_symmetry_nbd_refined 0.237 r_symmetry_xyhbond_nbd_refined 0.207 r_nbd_refined 0.204 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.147 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4315 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing