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Crystal structure of Adenylosuccinate Lyase from Leishmania major
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EFC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291.15 3 uL of protein solution at 10 mg.mL-1 (in a buffer containing 5 mM KPO4, 5 mM NaCl, 100 uM ADS) and 3 uL of reservoir solution (1.6 M ammonium sulfate, 0.1 M MES pH 6.5, 10% dioxane)
Crystal Properties Matthews coefficient Solvent content 3.14 60.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.02 α = 90 b = 130.02 β = 90 c = 316.77 γ = 90
Symmetry Space Group I 41 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 80 IMAGE PLATE MAR scanner 345 mm plate 2005-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 1.542
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.97 25.25 99.8 0.104 0.108 0.028 0.999 18.7 14.2 95392 30.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2 99.2 1.373 0.382 0.792
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.97 25.25 1.33 95009 4714 99.38 0.2122 0.2108 0.2102 0.2394 0.2393 42.56
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 15.1148 f_angle_d 0.9832 f_chiral_restr 0.0541 f_plane_restr 0.009 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7027 Nucleic Acid Atoms Solvent Atoms 415 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement PHENIX refinement iMOSFLM data reduction pointless data scaling PHASER phasing