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Crystal structure of native 6-phospho-glucosidase LpBgl from Lactobacillus plantarum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CMJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 15% (w/v) PEG 3350, 0.2 M di-ammonium phosphate, 0.1 M sodium
cacodylate, pH 6.4, 2 mM DTT and detergent CTAB.
Crystal Properties Matthews coefficient Solvent content 2.97 58.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 196.688 α = 90 b = 191.683 β = 102.75 c = 105.931 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 210r 2009-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 0.9794 ESRF BM16
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.48 61.233 94 0.117 0.14 0.076 0.987 6.9 3 126809 22.3
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) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.48 2.61 96.5 0.431 0.517 0.281 0.823 2.3 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT FREE R-VALUE 3CMJ 2.48 61.233 1.36 126790 6369 93.89 0.1618 0.1588 0.1619 0.2168 0.2188
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.298 f_angle_d 0.993 f_chiral_restr 0.057 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22392 Nucleic Acid Atoms Solvent Atoms 1605 Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALA data scaling PHASER phasing