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rhamnosidase from Klebsiella oxytoca with rhamnose bound
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 10% (w/v) PEG 3350, 200 mM MgSO4
Crystal Properties Matthews coefficient Solvent content 4.68 73.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.43 α = 90 b = 148.43 β = 90 c = 202.16 γ = 90
Symmetry Space Group P 41 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 PIXEL DECTRIS PILATUS 6M 2012-07-07 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS PILATUS 2M 2012-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 1.068 Diamond I24 2 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.920 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.7 63.07 98.5 0.125 0.061 0.995 9.7 4.9 61251 41.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.77 99 1.077 0.522 0.625 1.4 5 4450
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.7 63.07 58166 3084 97.97 0.1833 0.1823 0.2022 0.179 RANDOM 56.8
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] -1.16 -1.16 2.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.095 r_dihedral_angle_4_deg 18.189 r_dihedral_angle_3_deg 13.812 r_dihedral_angle_1_deg 5.518 r_mcangle_it 1.985 r_mcbond_it 1.225 r_mcbond_other 1.225 r_angle_refined_deg 1.134 r_angle_other_deg 0.811 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.095 r_dihedral_angle_4_deg 18.189 r_dihedral_angle_3_deg 13.812 r_dihedral_angle_1_deg 5.518 r_mcangle_it 1.985 r_mcbond_it 1.225 r_mcbond_other 1.225 r_angle_refined_deg 1.134 r_angle_other_deg 0.811 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8246 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 42
Software Software Software Name Purpose SHELX phasing REFMAC refinement PDB_EXTRACT data extraction Aimless data scaling