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rdpA dioxygenase holoenzyme
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 The protein solution was 10-20 mg/ml in 20mM Tris-pH 8, 50mM NaCl, 5mM bME. The precipitant solution was 0.1M Hepes-pH 7.5, 10(w/v)% PEG 8K, 8(v/v)% ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 3.45 64.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.014 α = 90 b = 153.014 β = 90 c = 156.845 γ = 90
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 MARMOSAIC 225 mm CCD 2009-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.000 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.3 109.6 100 0.113 23.5 6.9 79857
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 100 0.761 6.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.3 50 76047 3793 99.88 0.18782 0.18586 0.1908 0.22843 0.2265 RANDOM 45.479
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] 0.39 0.39 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.892 r_dihedral_angle_4_deg 19.682 r_dihedral_angle_3_deg 18.328 r_long_range_B_refined 10.331 r_long_range_B_other 10.325 r_dihedral_angle_1_deg 7.747 r_scangle_other 7.65 r_mcangle_other 7.023 r_mcangle_it 7.021 r_scbond_it 5.265
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.892 r_dihedral_angle_4_deg 19.682 r_dihedral_angle_3_deg 18.328 r_long_range_B_refined 10.331 r_long_range_B_other 10.325 r_dihedral_angle_1_deg 7.747 r_scangle_other 7.65 r_mcangle_other 7.023 r_mcangle_it 7.021 r_scbond_it 5.265 r_scbond_other 5.224 r_mcbond_it 4.81 r_mcbond_other 4.779 r_angle_refined_deg 1.975 r_angle_other_deg 1.212 r_chiral_restr 0.172 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 8891 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing