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Structure of E323L mutant of Homoprotocatechuate 2,3-Dioxygenase from Brevibacterium fuscum at 1.65A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IG9 PDB id 2IG9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 18% PEG8000, 0.1M Ca acetate, 0.1M Na cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.75 55.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.711 α = 90 b = 163.403 β = 90 c = 101.584 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 SBC-3 2007-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97903 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.65 50 97.2 0.061 0.061 18.734 4.4 220867 214697 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.71 96.5 0.469 0.469 1.647 3.8 21074
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB id 2IG9 1.65 23.46 203793 10782 97.22 0.1707 0.16946 0.1701 0.19429 RANDOM 19.372
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.815 r_dihedral_angle_4_deg 16.7 r_dihedral_angle_3_deg 12.738 r_dihedral_angle_1_deg 6.607 r_scangle_it 2.705 r_scbond_it 1.775 r_angle_refined_deg 1.302 r_mcangle_it 1.079 r_mcbond_it 0.707 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.815 r_dihedral_angle_4_deg 16.7 r_dihedral_angle_3_deg 12.738 r_dihedral_angle_1_deg 6.607 r_scangle_it 2.705 r_scbond_it 1.775 r_angle_refined_deg 1.302 r_mcangle_it 1.079 r_mcbond_it 0.707 r_nbtor_refined 0.303 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.199 r_symmetry_hbond_refined 0.175 r_xyhbond_nbd_refined 0.118 r_metal_ion_refined 0.101 r_chiral_restr 0.095 r_symmetry_metal_ion_refined 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11604 Nucleic Acid Atoms Solvent Atoms 1508 Heterogen Atoms 45
Software Software Software Name Purpose HKL-3000 data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling