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Structure of native Fe-containing Homoprotocatechuate 2,3-Dioxygenase at 1.70 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, 0.125 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 2.42 49.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.747 α = 90 b = 151.229 β = 90 c = 96.385 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 PIXEL PSI PILATUS 6M 2010-05-15 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315r 2010-03-21 M 3 1 x-ray 100 CCD ADSC QUANTUM 315r 2010-03-21 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9999 SLS X10SA 2 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1.7394 SOLEIL PROXIMA 1 3 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1.7428 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 1.7 89.43 98.3 0.064 0.104 8.6 3.4 177378 174363 3 18.3
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) 1.7 1.79 98.6 0.427 0.682 2 3.3 25338
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 59.49 165298 8613 97.86 0.16099 0.15957 0.1782 0.18796 0.204 RANDOM 20.596
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] 0.02 -0.04 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.953 r_dihedral_angle_4_deg 17.982 r_dihedral_angle_3_deg 12.739 r_dihedral_angle_1_deg 6.935 r_scangle_it 3.585 r_scbond_it 2.275 r_angle_refined_deg 1.461 r_mcangle_it 1.343 r_angle_other_deg 0.914 r_mcbond_it 0.772
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.953 r_dihedral_angle_4_deg 17.982 r_dihedral_angle_3_deg 12.739 r_dihedral_angle_1_deg 6.935 r_scangle_it 3.585 r_scbond_it 2.275 r_angle_refined_deg 1.461 r_mcangle_it 1.343 r_angle_other_deg 0.914 r_mcbond_it 0.772 r_mcbond_other 0.259 r_chiral_restr 0.098 r_bond_refined_d 0.015 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 11532 Nucleic Acid Atoms Solvent Atoms 1254 Heterogen Atoms 130
Software Software Software Name Purpose to data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling