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3D structure of Gan42B, a GH42 beta-galactosidase from G.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OJW PDB ENTRY 4OJW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 16-18% PEG 3350, 250 mM NaCl and 100 mM Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K
Crystal Properties Matthews coefficient Solvent content 2.66 53.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.84 α = 90 b = 181.35 β = 90 c = 196.57 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD ADSC QUANTUM 210 mirror 2010-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1
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 2.448 48.86 96.3 0.113 0.419 11.7 5.8 95492 91957
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 2.45 2.58 88.6 0.348 0.419 4.3 4.9
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION using phases from it's GanBE323A mutant PDB ENTRY 4OJW 2.448 48.859 1.35 91878 91872 4594 96.23 0.1365 0.1329 0.1362 0.2045 0.2062 13.375
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] -0.07 0.22 -0.15
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.426 f_angle_d 1.09 f_chiral_restr 0.041 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16922 Nucleic Acid Atoms Solvent Atoms 1504 Heterogen Atoms 153
Software Software Software Name Purpose PHENIX refinement REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling REFMAC phasing