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Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-29 (G206C, R207S, D210L, S211V)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZAL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M PCTP buffer pH 7.0, 25 % w/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.24 45.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.789 α = 90 b = 77.864 β = 90 c = 148.363 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 PIXEL RIGAKU HyPix-6000HE 2022-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.2 21.48 97.6 0.124 0.14 0.992 6.4 4.5 30380
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 99.2 0.496 0.555 0.902 1.9
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2ZAL 2.2 21.48 30354 1039 97.015 0.251 0.2494 0.3009 0.2934 37.081
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] 0.425 2.441 -2.866
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.657 r_dihedral_angle_4_deg 18.578 r_dihedral_angle_3_deg 16.717 r_dihedral_angle_1_deg 7.52 r_lrange_it 4.961 r_lrange_other 4.956 r_scangle_it 3.432 r_scangle_other 3.432 r_mcangle_other 3.183 r_mcangle_it 3.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.657 r_dihedral_angle_4_deg 18.578 r_dihedral_angle_3_deg 16.717 r_dihedral_angle_1_deg 7.52 r_lrange_it 4.961 r_lrange_other 4.956 r_scangle_it 3.432 r_scangle_other 3.432 r_mcangle_other 3.183 r_mcangle_it 3.182 r_scbond_it 2.277 r_scbond_other 2.277 r_mcbond_it 2.134 r_mcbond_other 2.132 r_angle_refined_deg 1.622 r_angle_other_deg 1.385 r_symmetry_xyhbond_nbd_refined 0.25 r_nbd_refined 0.197 r_nbd_other 0.196 r_xyhbond_nbd_refined 0.19 r_symmetry_nbd_other 0.188 r_metal_ion_refined 0.168 r_nbtor_refined 0.157 r_ncsr_local_group_1 0.104 r_symmetry_nbd_refined 0.091 r_symmetry_nbtor_other 0.084 r_ncsr_local_group_2 0.071 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.063 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4193 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling PHASER phasing