☰ Navigation Tabs
Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ_V72I mutant in complex with cyclopeptin (1b)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 100 mM TRIS/HCl, 1 M LiBr, 27% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.16 42.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.83 α = 90 b = 119.9 β = 90 c = 67.14 γ = 90
Symmetry Space Group C 2 2 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 2016-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 1.65 50 98 0.043 16.1 4.7 35034
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 1.65 1.75 99.5 0.549 2.3
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 (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 5DAP 1.65 15 33229 1749 97.85 0.14062 0.13873 0.1471 0.17392 0.1851 RANDOM 35
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] -1.66 2.75 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.966 r_sphericity_free 26.937 r_dihedral_angle_4_deg 16.887 r_dihedral_angle_3_deg 13.232 r_sphericity_bonded 8.872 r_dihedral_angle_1_deg 5.953 r_long_range_B_refined 3.284 r_long_range_B_other 2.878 r_mcangle_it 2.119 r_mcangle_other 2.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.966 r_sphericity_free 26.937 r_dihedral_angle_4_deg 16.887 r_dihedral_angle_3_deg 13.232 r_sphericity_bonded 8.872 r_dihedral_angle_1_deg 5.953 r_long_range_B_refined 3.284 r_long_range_B_other 2.878 r_mcangle_it 2.119 r_mcangle_other 2.119 r_scangle_other 2.088 r_scbond_it 1.821 r_scbond_other 1.82 r_mcbond_it 1.649 r_mcbond_other 1.648 r_angle_refined_deg 1.309 r_angle_other_deg 0.916 r_rigid_bond_restr 0.809 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2228 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing