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E. coli L-asparaginase II in complex with L-Asp at pH 5.6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 Crystals were grown in 0.17 M NH4-citrate, pH 5.6, 17-18% PEG3350, then soaked for 1 min in solution with 5 mM L-Asp
Crystal Properties Matthews coefficient Solvent content 2.06 40.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.178 α = 90 b = 62.395 β = 117.55 c = 140.665 γ = 90
Symmetry Space Group C 1 2 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 EIGER R 4M Multilayer X-ray mirrors VariMax HF 2018-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.6 40 88 0.019 0.024 0.013 21 2.5 135099
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 54.9 0.269 0.365 0.243 0.71 1.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.6 40 131536 3432 88.05 0.1318 0.1308 0.1418 0.1719 0.1801 RANDOM 20.616
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] 0.08 0.02 -0.11 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.362 r_dihedral_angle_4_deg 15.485 r_dihedral_angle_3_deg 13.147 r_dihedral_angle_1_deg 6.209 r_angle_refined_deg 1.939 r_angle_other_deg 1.075 r_chiral_restr 0.125 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.362 r_dihedral_angle_4_deg 15.485 r_dihedral_angle_3_deg 13.147 r_dihedral_angle_1_deg 6.209 r_angle_refined_deg 1.939 r_angle_other_deg 1.075 r_chiral_restr 0.125 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9670 Nucleic Acid Atoms Solvent Atoms 1725 Heterogen Atoms 46
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction