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Structure of Co-substituted Homoprotocatechuate 2,3-Dioxygenase from B.fuscum at 1.72 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 6.5 293 13% PEG6000, 0.1 M calcium chloride, 0.1 M Tris-HCl. Cryoprotectant 25% PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.43 49.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.539 α = 90 b = 152.075 β = 90 c = 96.491 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 ADSC QUANTUM 315r 2010-04-14 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315r 2010-03-21 M SINGLE WAVELENGTH 3 1 x-ray 100 CCD ADSC QUANTUM 315r 2010-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03 2 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1.6050 SOLEIL PROXIMA 1 3 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1.6077 SOLEIL PROXIMA 1
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 1,2,3 1.72 29.86 98.9 0.063 0.103 9 3.5 172043 170151 3 16.7
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) 1.72 1.81 98.7 0.437 1.9 3.5 24631
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 1.72 29.62 161661 8442 98.64 0.14814 0.14664 0.1656 0.17639 0.191 RANDOM 18.684
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 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.124 r_dihedral_angle_4_deg 18.473 r_dihedral_angle_3_deg 12.334 r_dihedral_angle_1_deg 7.15 r_scangle_it 3.06 r_scbond_it 2 r_angle_refined_deg 1.442 r_mcangle_it 1.116 r_angle_other_deg 0.915 r_mcbond_it 0.664
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.124 r_dihedral_angle_4_deg 18.473 r_dihedral_angle_3_deg 12.334 r_dihedral_angle_1_deg 7.15 r_scangle_it 3.06 r_scbond_it 2 r_angle_refined_deg 1.442 r_mcangle_it 1.116 r_angle_other_deg 0.915 r_mcbond_it 0.664 r_mcbond_other 0.225 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11523 Nucleic Acid Atoms Solvent Atoms 1651 Heterogen Atoms 130
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling