☰ Navigation Tabs
Dioxygenase AsqJ mutant (V72I) in complex with 2b and glycerol
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, SITTING DROP 8.2 293 100 mM HEPES/NaOH, 1.25 M LiBr, 26% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.22 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.98 α = 90 b = 121.24 β = 90 c = 67.32 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 2019-04-07 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 2 30 97.9 0.064 13.4 4.5 20394
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 2 2.1 0.653 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 2 30 19368 1019 97.82 0.1808 0.1795 0.1899 0.2056 0.2077 RANDOM 43.242
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] -0.97 1.98 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.4 r_dihedral_angle_4_deg 20.389 r_dihedral_angle_3_deg 14.904 r_dihedral_angle_1_deg 6.452 r_angle_refined_deg 1.267 r_angle_other_deg 1.085 r_rigid_bond_restr 0.315 r_chiral_restr 0.046 r_gen_planes_other 0.006 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.4 r_dihedral_angle_4_deg 20.389 r_dihedral_angle_3_deg 14.904 r_dihedral_angle_1_deg 6.452 r_angle_refined_deg 1.267 r_angle_other_deg 1.085 r_rigid_bond_restr 0.315 r_chiral_restr 0.046 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 r_bond_refined_d 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2219 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling REFMAC phasing