☰ Navigation Tabs
GH5-4 broad specificity endoglucanase from Ruminococcus champanellensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IM4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 Crystals were grown from protein solution mixed with an equal volume of reservoir solution, 0.5% Jeffamine, 100 mM HEES pH 7.0, and 1.1 pM Sodium Malonate H 7.0 (Hampton Index HT screen: C9) in a SD2 format microplate set with a TTP Labtech Mosquito robot. Crystals were cryoprotected with 1.0% Jeffamine, 100 mM HEES pH 7.0, 1.1 M Sodium Malonate pH 7.0, and 20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.33 47.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.98 α = 90 b = 85.85 β = 96.538 c = 87.2 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 300 mm CCD 2013-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.978560 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.6 45.37 97.62 0.1073 0.1242 0.06165 0.993 8.31 4.1 94298 17.19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.657 98.49 0.7174 0.8206 0.3954 0.681 1.54 4.2
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 4IM4 1.6 45.37 1.38 94068 2000 97.61 0.2038 0.2029 0.2034 0.2422 0.2432 20.67
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 12.276 f_angle_d 0.7898 f_chiral_restr 0.0483 f_bond_d 0.0055 f_plane_restr 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5551 Nucleic Acid Atoms Solvent Atoms 646 Heterogen Atoms 26
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing