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Crystal Structure of a sugar hydrolase (YeeB) from Lactococcus lactis, Northeast Structural Genomics Consortium Target KR108
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch, under oil 9.1 291 Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1 M TRIS (pH 9.1), 29% PEG400, and 0.1M (Mg)2SO4.
, microbatch, under oil, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.2 44.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.391 α = 90 b = 150.425 β = 90 c = 218.859 γ = 90
Symmetry Space Group C 2 2 21
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 4 mirrors 2008-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97907 NSLS X4A
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 3.2 30 92.6 0.088 0.082 17.4 5.1 38946 36064 1 1 54.6
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) 3.2 3.31 74.5 0.172 0.211 3.2 3 3883
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 3.2 19.96 2 2 35848 32873 3177 91.7 0.258 0.257 0.256 0.2733 0.296 0.3099 RANDOM 70.6
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] -14.28 -11.63 25.91
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_angle_deg 1.1 c_improper_angle_d 0.87 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8080 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction ADSC data collection DENZO data reduction SCALEPACK data scaling SnB phasing REFMAC refinement