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Crystal structure of an uncharacterized amidohydrolase from Saccharomyces cerevisiae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9 294 100mM Tris HCl pH 9, 32% PEG 4K, 200mM magnesium chloride hexahydrate, pH 9.0, Vapor diffusion, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.17 43.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.532 α = 90 b = 55.007 β = 95.85 c = 115.26 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 CCD MAR CCD 165 mm 2008-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97958 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.5 114.708 98.7 0.095 0.095 13.7 6.8 124867 123244 14
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 97.3 0.413 0.413 3.6 6.6 17650
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 1.5 15 124745 123161 6190 98.73 0.174 0.173 0.1769 0.199 0.2021 RANDOM 20.729
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] -0.38 -0.18 0.01 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.156 r_dihedral_angle_4_deg 13.338 r_dihedral_angle_3_deg 11.94 r_dihedral_angle_1_deg 5.365 r_scangle_it 3.361 r_scbond_it 2.314 r_mcangle_it 1.366 r_angle_refined_deg 1.238 r_mcbond_it 0.841 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.156 r_dihedral_angle_4_deg 13.338 r_dihedral_angle_3_deg 11.94 r_dihedral_angle_1_deg 5.365 r_scangle_it 3.361 r_scbond_it 2.314 r_mcangle_it 1.366 r_angle_refined_deg 1.238 r_mcbond_it 0.841 r_nbtor_refined 0.312 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.104 r_symmetry_hbond_refined 0.089 r_metal_ion_refined 0.088 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5793 Nucleic Acid Atoms Solvent Atoms 704 Heterogen Atoms 27
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXCD phasing SHELXE model building