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Asparaginase II from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IHD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.9 298 0.2 M Magnesium acetate tetrahydrate, 20% w/v Polyethylene glycol 3,350, L-Aspartic 1 mM
Crystal Properties Matthews coefficient Solvent content 2.04 39.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.989 α = 90 b = 60.162 β = 117.31 c = 151.108 γ = 90
Symmetry Space Group P 1 21 1
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 DECTRIS PILATUS 2M 2018-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.459 LNLS W01B-MX2
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 2.13 48.57 87.4 0.084 0.106 0.993 7.66 2.471 214114 39.599
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 2.13 2.26 65 0.358 0.46 0.762 2.09 2.168
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 1ihd 2.29 47.07 95186 4868 98.49 0.2265 0.2246 0.2207 0.2622 0.2543 RANDOM 36.614
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] -0.2 0.61 0.05 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.509 r_dihedral_angle_4_deg 18.191 r_dihedral_angle_3_deg 14.813 r_dihedral_angle_1_deg 6.632 r_angle_refined_deg 1.234 r_angle_other_deg 1.115 r_chiral_restr 0.04 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.509 r_dihedral_angle_4_deg 18.191 r_dihedral_angle_3_deg 14.813 r_dihedral_angle_1_deg 6.632 r_angle_refined_deg 1.234 r_angle_other_deg 1.115 r_chiral_restr 0.04 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19440 Nucleic Acid Atoms Solvent Atoms 615 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MrBUMP phasing PDB_EXTRACT data extraction