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Crystal structure of E. coli isoaspartyl aminopeptidase/L-asparaginase in complex with L-aspartate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K2X PDB entry 1K2X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 100mM Tris/HCl, 80mM calcium chloride, 100mM sodium aspartate, 17% PEG 4000, 13% PEG 400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.3 46.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.89 α = 90 b = 77.28 β = 90 c = 147.53 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH 2002-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.095 MAX II I711
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 1.9 20 95.8 0.064 15 3.5 43572 43572 -3 18.67
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 1.9 1.97 91.3 0.256 2.2 3 4085
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 R-free PDB entry 1K2X 1.9 20 42200 42200 1372 95.71 0.158 0.158 0.157 0.1698 0.188 0.1951 Random 13.27
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] 1.05 -0.36 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.92 r_scangle_it 3.91 r_scbond_it 2.29 r_angle_refined_deg 1.34 r_mcangle_it 1.25 r_angle_other_deg 0.83 r_mcbond_it 0.672 r_symmetry_vdw_refined 0.321 r_symmetry_vdw_other 0.311 r_nbd_other 0.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.92 r_scangle_it 3.91 r_scbond_it 2.29 r_angle_refined_deg 1.34 r_mcangle_it 1.25 r_angle_other_deg 0.83 r_mcbond_it 0.672 r_symmetry_vdw_refined 0.321 r_symmetry_vdw_other 0.311 r_nbd_other 0.243 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.144 r_symmetry_hbond_refined 0.135 r_metal_ion_refined 0.108 r_nbtor_other 0.085 r_chiral_restr 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4259 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing