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GH5-4 broad specificity endoglucanase from Clostridum cellulovorans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NDY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 26% PEG 3350 and 100 mM Bis-Tris pH 5.5
crystals were cryoprotected by supplementing crystallization reagent with 1.5% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.34 47.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.144 α = 90 b = 89.095 β = 90 c = 91.083 γ = 90
Symmetry Space Group P 21 21 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 MARMOSAIC 300 mm CCD 2013-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.978560 APS 21-ID-G
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 1.3 31.85 95.68 0.04056 0.04379 0.01633 0.999 29.24 7 85209 -3 10.14
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 1.3 1.346 78.27 0.2091 0.2333 0.09929 0.956 7.53 5.3
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 3NDY 1.3 25.09 1.36 85208 2099 95.66 0.1267 0.1263 0.1271 0.1422 0.1436 13.53
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 11.952 f_angle_d 0.9896 f_chiral_restr 0.0836 f_plane_restr 0.0073 f_bond_d 0.0072
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2672 Nucleic Acid Atoms Solvent Atoms 556 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing