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Crystal structure of Human aromatic L-amino acid decarboxylase (AADC) in the open conformation with LLP and PLP bound to Chain-A and Chain-B respectively
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RBF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 vapor diffusion, soaking 7 294 crystals obtained from holoAADC in 0.1 M HEPES pH 7.0, 28-30% Jeffamine ED 2001 pH 7.0 were transferred in a ML droplet containing 10mM PLP to yield crystals with PLP and LLP bound, vapor diffusion, soaking, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.71 54.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177 α = 90 b = 177 β = 90 c = 74.83 γ = 90
Symmetry Space Group P 41 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 4r 2010-11-20 M SINGLE WAVELENGTH 2 1 3 1 4 1 5 1 6 1 7 1 8 1 9 1 10 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 125.158 100 0.133 13.6 7.1 29907 29907 2 2
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 2.8 2.95 100 0.612 0.612 1.2 7.2 4285
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3RBF 2.8 30 29867 29803 1513 99.91 0.266 0.2034 0.2005 0.2147 0.2586 0.2595 RANDOM 56.159
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] 0.91 0.91 -1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.887 r_dihedral_angle_3_deg 20.483 r_dihedral_angle_4_deg 18.452 r_dihedral_angle_1_deg 5.808 r_scangle_it 3.049 r_scbond_it 1.78 r_angle_refined_deg 1.326 r_mcangle_it 1.227 r_mcbond_it 0.63 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.887 r_dihedral_angle_3_deg 20.483 r_dihedral_angle_4_deg 18.452 r_dihedral_angle_1_deg 5.808 r_scangle_it 3.049 r_scbond_it 1.78 r_angle_refined_deg 1.326 r_mcangle_it 1.227 r_mcbond_it 0.63 r_chiral_restr 0.102 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6966 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 16
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction