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Structure of Mn-substituted Homoprotocatechuate 2,3-Dioxygenase at 1.65 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 49.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.542 α = 90 b = 151.497 β = 90 c = 96.359 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 2010-08-04 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315r 2010-08-04 M SINGLE WAVELENGTH 3 1 x-ray 100 CCD ADSC QUANTUM 315r 2010-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03 2 SYNCHROTRON DIAMOND BEAMLINE I03 1.8923 Diamond I03 3 SYNCHROTRON DIAMOND BEAMLINE I03 1.8958 Diamond I03
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 1.65 29.78 97.6 0.061 0.094 7.3 3.2 193414 188772 3 16.4
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) 1.65 1.74 98.5 0.357 0.552 2 3.2 27593
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 1.65 29.77 179300 9422 97.25 0.14932 0.14789 0.1662 0.17662 0.1908 RANDOM 20.512
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] -0.03 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.617 r_dihedral_angle_4_deg 17.656 r_dihedral_angle_3_deg 11.996 r_dihedral_angle_1_deg 6.93 r_scangle_it 3.315 r_scbond_it 2.091 r_angle_refined_deg 1.403 r_mcangle_it 1.236 r_angle_other_deg 0.902 r_mcbond_it 0.717
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.617 r_dihedral_angle_4_deg 17.656 r_dihedral_angle_3_deg 11.996 r_dihedral_angle_1_deg 6.93 r_scangle_it 3.315 r_scbond_it 2.091 r_angle_refined_deg 1.403 r_mcangle_it 1.236 r_angle_other_deg 0.902 r_mcbond_it 0.717 r_mcbond_other 0.232 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11532 Nucleic Acid Atoms Solvent Atoms 1379 Heterogen Atoms 143
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling