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Structure of alfa-galactosidase (MEL1) from Saccharomyces cerevisiae
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 2.69 54.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.243 α = 90 b = 101.243 β = 90 c = 111.521 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 2009-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.979 ESRF ID23-1
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 1.95 111.521 100 0.067 0.067 7.6 10.6 42919 27.8
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) 1.95 2.06 100 0.457 0.457 1.7 12 6150
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 1.95 111.52 42892 2163 100 0.205 0.204 0.2038 0.234 0.2321 RANDOM 28.367
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] -0.2 -0.2 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.947 r_dihedral_angle_4_deg 15.83 r_dihedral_angle_3_deg 14.618 r_dihedral_angle_1_deg 5.8 r_scangle_it 2.137 r_scbond_it 1.542 r_angle_refined_deg 1.372 r_mcangle_it 0.849 r_mcbond_it 0.508 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.947 r_dihedral_angle_4_deg 15.83 r_dihedral_angle_3_deg 14.618 r_dihedral_angle_1_deg 5.8 r_scangle_it 2.137 r_scbond_it 1.542 r_angle_refined_deg 1.372 r_mcangle_it 0.849 r_mcbond_it 0.508 r_nbtor_refined 0.306 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3518 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms 145
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOLREP phasing