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Crystal structure of p-coumaric acid decarboxylase (NP_786857.1) from Lactobacillus plantarum at 1.70 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 4 277 2.4M (NH4)2SO4, 0.1M Citrate pH 4.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.16 42.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.17 α = 90 b = 64.17 β = 90 c = 83.12 γ = 120
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 315 Flat mirror (vertical focusing) 2006-02-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.918370, 0.979035 SSRL BL11-1
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 1.7 27.79 99.1 0.087 7.45 3.81 41971 14
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 1.7 1.76 94.6 82 0.487 1.78
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.7 27.79 42001 2125 99.81 0.177 0.17682 0.175 0.212 0.1621 RANDOM 12.824
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] 0.38 0.19 0.38 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.862 r_dihedral_angle_3_deg 11.737 r_dihedral_angle_4_deg 8.858 r_dihedral_angle_1_deg 6.616 r_scangle_it 3.843 r_scbond_it 2.932 r_mcangle_it 1.491 r_angle_refined_deg 1.128 r_mcbond_it 1.095 r_angle_other_deg 0.719
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.862 r_dihedral_angle_3_deg 11.737 r_dihedral_angle_4_deg 8.858 r_dihedral_angle_1_deg 6.616 r_scangle_it 3.843 r_scbond_it 2.932 r_mcangle_it 1.491 r_angle_refined_deg 1.128 r_mcbond_it 1.095 r_angle_other_deg 0.719 r_mcbond_other 0.261 r_symmetry_vdw_refined 0.213 r_nbd_refined 0.179 r_nbtor_refined 0.179 r_symmetry_vdw_other 0.171 r_nbd_other 0.167 r_symmetry_hbond_refined 0.149 r_xyhbond_nbd_refined 0.123 r_nbtor_other 0.08 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2797 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 153
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing