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Crystal Structure of p-coumaric Acid Decarboxylase from Lactobacillus plantarum: structural insights into the active site and decarboxylation catalytic mechanism
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GC9 PDB ENTRY 2GC9
Crystallization Crystal Properties Matthews coefficient Solvent content 2.6 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.181 α = 90 b = 43.181 β = 90 c = 232.498 γ = 90
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 CCD 2007-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.38 46.5 100 0.11 13 7.2 86850
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 1.38 1.45 100 0.54 2.8 7.2
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 2GC9 1.38 40.49 82379 4348 100 0.192 0.191 0.189 0.209 0.2075 RANDOM 13.31
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 33.359 r_dihedral_angle_4_deg 14.457 r_dihedral_angle_3_deg 11.81 r_dihedral_angle_1_deg 6.048 r_scangle_it 1.344 r_angle_refined_deg 1.022 r_scbond_it 0.877 r_mcangle_it 0.676 r_mcbond_it 0.422 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.359 r_dihedral_angle_4_deg 14.457 r_dihedral_angle_3_deg 11.81 r_dihedral_angle_1_deg 6.048 r_scangle_it 1.344 r_angle_refined_deg 1.022 r_scbond_it 0.877 r_mcangle_it 0.676 r_mcbond_it 0.422 r_nbtor_refined 0.308 r_nbd_refined 0.181 r_symmetry_hbond_refined 0.158 r_symmetry_vdw_refined 0.104 r_xyhbond_nbd_refined 0.077 r_chiral_restr 0.073 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2918 Nucleic Acid Atoms Solvent Atoms 566 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing