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Crystal structure of cleaved L-aspartate-alpha-decarboxylase from Francisella tularensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 0.2 M Lithium sulfate, 0.1 M Bis-Tris, 25% PeG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.61 52.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.934 α = 90 b = 80.525 β = 104.33 c = 85.025 γ = 90
Symmetry Space Group P 1 21 1
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 315r mirrors 2009-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-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 1.55 40 99.7 0.071 27.6 3.7 151160 150740 2 2
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) 1.55 1.58 99.7 0.663
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 SAD with MR THROUGHOUT 2C45 1.55 28.66 2 2 150301 149429 972 99.44 0.18 0.17196 0.17179 0.1804 0.19704 0.2068 RANDOM 17.715
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] 0.02 -0.02 -0.08 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.997 r_dihedral_angle_3_deg 12.221 r_dihedral_angle_4_deg 9.872 r_dihedral_angle_1_deg 6.328 r_scangle_it 4.555 r_scbond_it 2.646 r_mcangle_it 1.92 r_angle_refined_deg 1.51 r_angle_other_deg 1.066 r_mcbond_it 1.028
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.997 r_dihedral_angle_3_deg 12.221 r_dihedral_angle_4_deg 9.872 r_dihedral_angle_1_deg 6.328 r_scangle_it 4.555 r_scbond_it 2.646 r_mcangle_it 1.92 r_angle_refined_deg 1.51 r_angle_other_deg 1.066 r_mcbond_it 1.028 r_mcbond_other 0.193 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6662 Nucleic Acid Atoms Solvent Atoms 891 Heterogen Atoms 44
Software Software Software Name Purpose SBC-Collect data collection Auto-Rickshaw phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling