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Crystal structure of aspartase from Bacillus sp. YM55-1 with bound L-aspartate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J3U PDB ENTRY 1J3U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 0.25 M NaSCN, 10 mM CaCl2, 0.1 M HEPES, pH 7.0, 20% PEG3350, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3 58.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.853 α = 89.93 b = 118.96 β = 89.93 c = 141.414 γ = 76.42
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 210 2009-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 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 2.6 141.414 97.9 0.108 8 2.1 144679 144679
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 2.6 2.74 97.4 0.505 0.505 1.5 2.1 21005
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 1J3U 2.6 39.73 144669 7250 97.9 0.1956 0.1928 0.1943 0.2502 0.2487 RANDOM 34.5829
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] 0.12 0.02 -0.02 0.42 0.03 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.805 r_dihedral_angle_4_deg 18.665 r_dihedral_angle_3_deg 17.605 r_dihedral_angle_1_deg 5.083 r_scangle_it 2.063 r_angle_refined_deg 1.19 r_scbond_it 1.185 r_mcangle_it 0.82 r_mcbond_it 0.424 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.805 r_dihedral_angle_4_deg 18.665 r_dihedral_angle_3_deg 17.605 r_dihedral_angle_1_deg 5.083 r_scangle_it 2.063 r_angle_refined_deg 1.19 r_scbond_it 1.185 r_mcangle_it 0.82 r_mcbond_it 0.424 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28473 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 22
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing