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Orthorhombic crystal structure of precursor E. coli isoaspartyl peptidase/L-asparaginase (EcAIII) with active-site T179A mutation
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 200mM MgCl2, 100mM Tris/HCl, 15% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.22 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.35 α = 90 b = 77.78 β = 90 c = 147.93 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 MARMOSAIC 225 mm CCD 2007-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 1.000 EMBL/DESY, HAMBURG X12
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 2 25 94 0.103 9.2 3 38010 38010 -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 2 2.07 69.1 0.4 2.1 2.1
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 (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 1K2X 2.01 25 36440 36439 1524 93.72 0.19961 0.19741 0.1964 0.25285 0.2487 RANDOM 23.628
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] 4.84 -2.37 -2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.743 r_dihedral_angle_4_deg 16.541 r_dihedral_angle_3_deg 14.579 r_dihedral_angle_1_deg 6.386 r_scangle_it 3.085 r_scbond_it 2.063 r_angle_refined_deg 1.548 r_mcangle_it 1.099 r_mcbond_it 0.688 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.743 r_dihedral_angle_4_deg 16.541 r_dihedral_angle_3_deg 14.579 r_dihedral_angle_1_deg 6.386 r_scangle_it 3.085 r_scbond_it 2.063 r_angle_refined_deg 1.548 r_mcangle_it 1.099 r_mcbond_it 0.688 r_nbtor_refined 0.298 r_symmetry_vdw_refined 0.248 r_symmetry_hbond_refined 0.245 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.144 r_metal_ion_refined 0.112 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4286 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing