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Crystal Structure of an Aspartoacylase from Rattus norvegicus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 MES PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (1.9 M Ammonium sulfate, 0.10 M HEPPS PH 8.5). Crystal cryo-protected with well solution supplemented with a final
concentration of 30% Ethylene glycol, temperature 293K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.33 47.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.581 α = 90 b = 135.778 β = 101.49 c = 54.033 γ = 90
Symmetry Space Group C 1 2 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 MARMOSAIC 300 mm CCD Adjustable focusing mirrors in K-B geometry 2006-04-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97928, 0.95373 APS 23-ID-D
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 1.8 80 97.5 0.093 9.949 7.1 58208
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 1.8 1.84 86.6 0.47 2.167 4.2 3424
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-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.805 41.75 58208 2955 97.248 0.152 0.1494 0.194 0.221 Random 21.762
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] 0.168 0.118 0.098 -0.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.806 r_dihedral_angle_3_deg 14.561 r_dihedral_angle_4_deg 14.525 r_scangle_it 7.024 r_dihedral_angle_1_deg 5.845 r_scbond_it 5.098 r_mcangle_it 2.992 r_mcbond_it 1.868 r_angle_refined_deg 1.616 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.806 r_dihedral_angle_3_deg 14.561 r_dihedral_angle_4_deg 14.525 r_scangle_it 7.024 r_dihedral_angle_1_deg 5.845 r_scbond_it 5.098 r_mcangle_it 2.992 r_mcbond_it 1.868 r_angle_refined_deg 1.616 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.215 r_symmetry_vdw_refined 0.21 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.124 r_bond_refined_d 0.02 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4862 Nucleic Acid Atoms Solvent Atoms 552 Heterogen Atoms 27
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction SHELXE model building ARP/wARP model building