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Crystal Structure of Phenolic Acid Decarboxylase from Bacillus pumilus UI-670
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P8G PDB ENTRY 2P8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 293 0.2 M Na/K tartarate, 0.1 M tri-sodium citrate, 0.5 M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.01 59.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.107 α = 90 b = 109.964 β = 90 c = 45.428 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 Rayonix 225 HE 2008-06-04 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 1.69 50 99.1 0.095 10.5 5.9 52226
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 1.69 1.75 95.7 0.603 4.9 4990
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 2P8G 1.69 50 52132 2653 98.7 0.186 0.185 0.1852 0.204 0.2032 RANDOM 19.448
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] 0.78 -0.86 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.524 r_dihedral_angle_3_deg 11.289 r_dihedral_angle_4_deg 7.795 r_dihedral_angle_1_deg 6.182 r_scangle_it 3.047 r_scbond_it 1.782 r_angle_refined_deg 1.059 r_mcangle_it 1.046 r_mcbond_it 0.522 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.524 r_dihedral_angle_3_deg 11.289 r_dihedral_angle_4_deg 7.795 r_dihedral_angle_1_deg 6.182 r_scangle_it 3.047 r_scbond_it 1.782 r_angle_refined_deg 1.059 r_mcangle_it 1.046 r_mcbond_it 0.522 r_chiral_restr 0.08 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2666 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing