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Hexagonal 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 7.5 292 4.3M NaCl, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 5.2 76.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.47 α = 90 b = 149.47 β = 90 c = 214.35 γ = 120
Symmetry Space Group P 61 2 2
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 2007-02-03 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 1.95 47.67 96.6 0.107 14.3 5.9 98405 98405 -3 27.3
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 1.95 2.06 98.5 0.76 2.2 5.2 14515
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 R-FREE PDB entry 1K2X 1.95 44.51 97402 97402 992 95.75 0.184 0.184 0.1859 0.203 0.2048 RANDOM 27.62
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] -1.66 -0.83 -1.66 2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.939 r_dihedral_angle_4_deg 12.949 r_dihedral_angle_3_deg 12.576 r_dihedral_angle_1_deg 5.876 r_scangle_it 3.162 r_scbond_it 1.967 r_angle_refined_deg 1.399 r_mcangle_it 1.11 r_angle_other_deg 0.948 r_mcbond_it 0.631
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.939 r_dihedral_angle_4_deg 12.949 r_dihedral_angle_3_deg 12.576 r_dihedral_angle_1_deg 5.876 r_scangle_it 3.162 r_scbond_it 1.967 r_angle_refined_deg 1.399 r_mcangle_it 1.11 r_angle_other_deg 0.948 r_mcbond_it 0.631 r_symmetry_hbond_refined 0.324 r_symmetry_vdw_other 0.309 r_nbd_refined 0.227 r_nbd_other 0.195 r_nbtor_refined 0.174 r_mcbond_other 0.174 r_xyhbond_nbd_refined 0.138 r_metal_ion_refined 0.138 r_nbtor_other 0.09 r_chiral_restr 0.083 r_symmetry_vdw_refined 0.06 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4442 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling PHASER phasing