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Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PCD A TRUNCATED MODEL MADE FROM PDB ID = 2PCD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 277 1.5-1.8 M ammonium sulfate, 2-5 mM beta-mercaptoethanol, and 40-60 mM TRIS-HCl pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.58 52.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.311 α = 90 b = 140.487 β = 90 c = 168.061 γ = 90
Symmetry Space Group I 2 2 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 MIRRORS 2009-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.59 50 99.5 0.043 20.7 5.4 199921 3 17.4
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 1.59 1.62 97.2 0.291 4.6 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 A TRUNCATED MODEL MADE FROM PDB ID = 2PCD 1.59 30.6 1 199921 199608 10063 99.1 0.148 0.146 0.1519 0.167 0.1726 RANDOM 19.98
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.325 r_dihedral_angle_4_deg 16.196 r_dihedral_angle_3_deg 12.329 r_dihedral_angle_1_deg 6.44 r_scangle_it 3.383 r_scbond_it 2.108 r_angle_refined_deg 1.436 r_mcangle_it 1.356 r_mcbond_it 0.773 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.325 r_dihedral_angle_4_deg 16.196 r_dihedral_angle_3_deg 12.329 r_dihedral_angle_1_deg 6.44 r_scangle_it 3.383 r_scbond_it 2.108 r_angle_refined_deg 1.436 r_mcangle_it 1.356 r_mcbond_it 0.773 r_chiral_restr 0.104 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10374 Nucleic Acid Atoms Solvent Atoms 1602 Heterogen Atoms 138
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction