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Structure of a full-length Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in a new spacegroup.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F1X PDB entry 1F1X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 18% PEG8000, 0.2 M calcium acetate, 0.1 M sodium cacodylate. Prior to freezing in liquid nitrogen, crystals were sequentially transferred into mother liquor solutions containing 5, 10, 15, and then 20% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.29 45.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.445 α = 90 b = 152.802 β = 90 c = 99.714 γ = 90
Symmetry Space Group P 21 21 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 NOIR-1 2005-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.23983 ALS 4.2.2
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 1.9 53.15 99.8 0.099 7.1 3.18 133141 132886
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 1.9 1.97 99.9 0.532 2 3.1 13150
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1F1X 1.9 46.08 132683 132683 6680 99.67 0.18976 0.1874 0.1887 0.23443 0.2353 RANDOM 23.337
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.881 r_dihedral_angle_4_deg 17.693 r_dihedral_angle_3_deg 13.19 r_dihedral_angle_1_deg 7.036 r_scangle_it 3.065 r_scbond_it 2.084 r_angle_refined_deg 1.455 r_mcangle_it 1.166 r_mcbond_it 0.956 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.881 r_dihedral_angle_4_deg 17.693 r_dihedral_angle_3_deg 13.19 r_dihedral_angle_1_deg 7.036 r_scangle_it 3.065 r_scbond_it 2.084 r_angle_refined_deg 1.455 r_mcangle_it 1.166 r_mcbond_it 0.956 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.223 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.189 r_symmetry_metal_ion_refined 0.165 r_xyhbond_nbd_refined 0.148 r_metal_ion_refined 0.105 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11600 Nucleic Acid Atoms Solvent Atoms 1248 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection d*TREK data reduction d*TREK data scaling CCP4 phasing