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Structure of alfa-galactosidase (MEL1) from Saccharomyces cerevisiae with melibiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UAS PDB ENTRY 1UAS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 Deglycosylated sample. 19% PEG3350, 0.1 M BisTris, 0.2 M SCNK, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.66 53.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.729 α = 90 b = 100.729 β = 90 c = 111.28 γ = 90
Symmetry Space Group P 4 21 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 2009-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 2.4 111.28 99.6 0.111 0.111 6.7 10.4 22940 32.2
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) 2.4 2.53 99.2 0.433 0.433 5.8 10.1 3262
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 1UAS 2.4 59.99 21747 1174 99.47 0.20131 0.19849 0.2001 0.25336 0.2498 RANDOM 26.253
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] 0.73 0.73 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.826 r_dihedral_angle_4_deg 19.22 r_dihedral_angle_3_deg 15.453 r_dihedral_angle_1_deg 6.121 r_scangle_it 2.806 r_scbond_it 1.931 r_angle_refined_deg 1.546 r_mcangle_it 1.163 r_mcbond_it 0.608 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.826 r_dihedral_angle_4_deg 19.22 r_dihedral_angle_3_deg 15.453 r_dihedral_angle_1_deg 6.121 r_scangle_it 2.806 r_scbond_it 1.931 r_angle_refined_deg 1.546 r_mcangle_it 1.163 r_mcbond_it 0.608 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.238 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3518 Nucleic Acid Atoms Solvent Atoms 415 Heterogen Atoms 136
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling