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Structure of Mn-substituted Homoprotocatechuate 2,3-Dioxygenase from B.fuscum at 1.7 Ang resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IG9 PDB entry 2IG9
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, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.42 49.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.502 α = 90 b = 152.191 β = 90 c = 96.278 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 2007-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97857 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 1.7 55 99.3 0.088 0.088 15.308 4.7 167766
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 1.7 1.76 98.4 0.555 2.258 3.8 17278
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 2IG9 1.7 28.82 167766 8849 99.32 0.17174 0.17041 0.1733 0.19671 0.1992 RANDOM 21.204
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 32.166 r_dihedral_angle_4_deg 16.395 r_dihedral_angle_3_deg 12.311 r_dihedral_angle_1_deg 6.742 r_scangle_it 2.666 r_scbond_it 1.76 r_angle_refined_deg 1.297 r_mcangle_it 1.024 r_mcbond_it 0.682 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.166 r_dihedral_angle_4_deg 16.395 r_dihedral_angle_3_deg 12.311 r_dihedral_angle_1_deg 6.742 r_scangle_it 2.666 r_scbond_it 1.76 r_angle_refined_deg 1.297 r_mcangle_it 1.024 r_mcbond_it 0.682 r_nbtor_refined 0.306 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.178 r_symmetry_hbond_refined 0.171 r_symmetry_metal_ion_refined 0.134 r_metal_ion_refined 0.121 r_xyhbond_nbd_refined 0.107 r_chiral_restr 0.096 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11600 Nucleic Acid Atoms Solvent Atoms 1244 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing