☰ Navigation Tabs
UndA, an oxygen-activating, non-heme iron dependent desaturase/decarboxylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OQL PDB entry 3OQL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 298 0.1 M MES, 1.8 M ammonium sulfate, 0.2 mM iron(II) ammonium sulfate, pH 6.5-7.0
Crystal Properties Matthews coefficient Solvent content 4.28 71.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.38 α = 90 b = 218.44 β = 90 c = 67.31 γ = 90
Symmetry Space Group C 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2013-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 0.999 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 118.69 99.9 9.7 4.4 82394 82274
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 99.99 4.3
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 PDB entry 3OQL 1.9 118.69 78154 4120 99.8 0.14724 0.14469 0.1572 0.19577 0.2063 RANDOM 35.365
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] -0.11 -0.06 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.081 r_sphericity_free 28.621 r_dihedral_angle_4_deg 19.557 r_dihedral_angle_3_deg 15.516 r_sphericity_bonded 15.081 r_long_range_B_refined 7.865 r_scangle_other 7.703 r_long_range_B_other 7.665 r_scbond_it 7.233 r_scbond_other 7.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.081 r_sphericity_free 28.621 r_dihedral_angle_4_deg 19.557 r_dihedral_angle_3_deg 15.516 r_sphericity_bonded 15.081 r_long_range_B_refined 7.865 r_scangle_other 7.703 r_long_range_B_other 7.665 r_scbond_it 7.233 r_scbond_other 7.14 r_mcangle_other 6.551 r_mcangle_it 6.546 r_rigid_bond_restr 6.336 r_mcbond_it 5.772 r_mcbond_other 5.761 r_dihedral_angle_1_deg 5.651 r_angle_refined_deg 1.998 r_angle_other_deg 1.034 r_chiral_restr 0.133 r_bond_other_d 0.052 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 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 4170 Nucleic Acid Atoms Solvent Atoms 545 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement PHENIX refinement MOSFLM data reduction SCALA data scaling PHASER phasing