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Crystal structure of Allantoicase (yir029w) from Saccharomyces cerevisiae at 2.40 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 293 30% Ethylene Glycol , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K 2 VAPOR DIFFUSION,SITTING DROP,NANODROP 293 30% Ethylene Glycol, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.209 α = 90 b = 107.209 β = 90 c = 134.918 γ = 120
Symmetry Space Group P 63 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 100 CCD ADSC QUANTUM 315 2003-04-17 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2003-04-17 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1 2 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979608, 0.918370, 0.979413 SSRL BL9-2
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 1,2 2.4 54.554 99.8 0.099 13 5.1 18532 18532 56.4
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) 1,2 2.4 2.46 98.8 0.707 1.8 2.6 1325
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 MAD THROUGHOUT 2.4 41.97 17676 830 99.77 0.17765 0.17542 0.1868 0.22238 0.2294 RANDOM 57.277
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] -2.4 -1.2 -2.4 3.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.267 r_dihedral_angle_4_deg 17.963 r_dihedral_angle_3_deg 17.738 r_dihedral_angle_1_deg 7.304 r_scangle_it 2.603 r_scbond_it 1.706 r_angle_refined_deg 1.505 r_mcangle_it 1.285 r_angle_other_deg 0.832 r_mcbond_it 0.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.267 r_dihedral_angle_4_deg 17.963 r_dihedral_angle_3_deg 17.738 r_dihedral_angle_1_deg 7.304 r_scangle_it 2.603 r_scbond_it 1.706 r_angle_refined_deg 1.505 r_mcangle_it 1.285 r_angle_other_deg 0.832 r_mcbond_it 0.832 r_symmetry_vdw_other 0.302 r_nbd_other 0.199 r_nbd_refined 0.185 r_symmetry_hbond_refined 0.164 r_symmetry_vdw_refined 0.148 r_chiral_restr 0.093 r_nbtor_other 0.091 r_xyhbond_nbd_refined 0.022 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2548 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling SOLVE phasing RESOLVE model building REFMAC refinement CCP4 data scaling RESOLVE phasing