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Crystal structure analysis of the cold-adamped beta-galactosidase from Rahnella sp. R3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8 293 0.2 M sodium acetate, 0.1 M Tris-HCl, 30%(w/v) PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.52 51.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.426 α = 90 b = 106.831 β = 109 c = 164.244 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 MARMOSAIC 325 mm CCD 2014-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.561 138.448 98.6 0.116 0.163 0.085 8.6 3.5 151929 151929
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.56 2.7 96.8 0.485 0.485 0.349 1.6 3.2 21717
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 THROUGHOUT 2.561 138.448 149793 2020 98.46 0.2 0.1993 0.2043 0.2468 0.2485 RANDOM 32.339
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] 1.95 -0.13 -3.64 1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.773 r_dihedral_angle_4_deg 19.798 r_dihedral_angle_3_deg 15.361 r_dihedral_angle_1_deg 7.051 r_mcangle_it 2.912 r_mcbond_it 1.856 r_mcbond_other 1.855 r_angle_refined_deg 1.555 r_angle_other_deg 1.007 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.773 r_dihedral_angle_4_deg 19.798 r_dihedral_angle_3_deg 15.361 r_dihedral_angle_1_deg 7.051 r_mcangle_it 2.912 r_mcbond_it 1.856 r_mcbond_other 1.855 r_angle_refined_deg 1.555 r_angle_other_deg 1.007 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32507 Nucleic Acid Atoms Solvent Atoms 428 Heterogen Atoms 30
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction