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Crystal structure of dioxygenase Tetur07g02040
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.2 M LiSO4, 0.1 M HEPES pH 7.5, 10%w/v PEG3350, 10 mM catechol
Crystal Properties Matthews coefficient Solvent content 2.06 40.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.091 α = 90 b = 45.415 β = 94.29 c = 83.04 γ = 90
Symmetry Space Group P 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 CCD RAYONIX MX300-HS 2017-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.15 40 95.3 0.056 0.056 0.064 0.032 32 4 24133 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19 72.3 0.252 0.252 0.3 0.16 0.963 3.4 3.1
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.15 40 22883 1095 95.58 0.21592 0.21429 0.24827 0.2594 RANDOM 66.448
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] -3.23 -0.6 5.61 -2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.401 r_dihedral_angle_4_deg 13.491 r_dihedral_angle_3_deg 13.04 r_dihedral_angle_1_deg 6.687 r_long_range_B_refined 5.624 r_long_range_B_other 5.614 r_angle_other_deg 3.838 r_mcangle_it 3.109 r_mcangle_other 3.109 r_scangle_other 2.922
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.401 r_dihedral_angle_4_deg 13.491 r_dihedral_angle_3_deg 13.04 r_dihedral_angle_1_deg 6.687 r_long_range_B_refined 5.624 r_long_range_B_other 5.614 r_angle_other_deg 3.838 r_mcangle_it 3.109 r_mcangle_other 3.109 r_scangle_other 2.922 r_mcbond_other 1.893 r_mcbond_it 1.892 r_scbond_it 1.771 r_scbond_other 1.77 r_angle_refined_deg 1.588 r_chiral_restr 0.1 r_bond_refined_d 0.011 r_gen_planes_other 0.009 r_gen_planes_refined 0.007 r_bond_other_d 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3153 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing