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Conformational dynamics of aspartate alpha-decarboxylase active site revealed by protein-ligand complexes: 1-methyl-L-aspartate complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AW8 PDB ENTRY 1AW8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.2 5 MG/ML ASPARTATE-ALPHA-DECARBOXYLASE IN 1.5 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE, PH 3.8
Crystal Properties Matthews coefficient Solvent content 2.47 50.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.022 α = 90 b = 71.022 β = 90 c = 216.376 γ = 120
Symmetry Space Group P 61 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 PIXEL DECTRIS PILATUS 6M 2011-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24
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 1.5 59.16 99.8 0.05 33.8 19 52794 17.3
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 1.5 1.58 98.6 0.52 6.2 18.8
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 1AW8 1.5 61.51 49995 2682 99.79 0.136 0.135 0.1372 0.162 0.1627 RANDOM 17.674
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] -0.31 -0.15 -0.31 0.46
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 30.305 r_dihedral_angle_2_deg 29.364 r_dihedral_angle_3_deg 13.704 r_sphericity_bonded 13.004 r_dihedral_angle_4_deg 12.265 r_rigid_bond_restr 8.535 r_dihedral_angle_1_deg 6.769 r_angle_refined_deg 2.51 r_angle_other_deg 1.472 r_chiral_restr 0.187
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 30.305 r_dihedral_angle_2_deg 29.364 r_dihedral_angle_3_deg 13.704 r_sphericity_bonded 13.004 r_dihedral_angle_4_deg 12.265 r_rigid_bond_restr 8.535 r_dihedral_angle_1_deg 6.769 r_angle_refined_deg 2.51 r_angle_other_deg 1.472 r_chiral_restr 0.187 r_bond_refined_d 0.029 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.003 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1865 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing