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Crystal structure of potassium-dependent plant-type L-asparaginase from Phaseolus vulgaris in complex with K+ and Na+ cations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PU6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 20% PEG3350, 0.1M bis tris propane, 0.2M sodium nitrate , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.61 52.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.885 α = 90 b = 102.632 β = 90 c = 123.754 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 RAYONIX MX-225 2012-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.827 BESSY 14.2
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 1.79 38.77 99.1 0.053 16.33 4.1 68445 68445 -3 33.3
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 1.79 1.89 98.2 0.63 1.98 4.1 10836
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 (All) 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 4PU6 1.79 38.77 68445 68445 1232 99.1 0.1643 0.1643 0.1635 0.1648 0.2066 0.2069 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.302 f_angle_d 1.373 f_chiral_restr 0.097 f_bond_d 0.019 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4228 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 92
Software Software Software Name Purpose MAR345 data collection PHASER phasing PHENIX refinement XDS data reduction XSCALE data scaling