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Crystal structure of an endoglucanase from Penicillium verruculosum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GZJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 285 20 % w/v Polyethylene glycol 6,000 50 mM BIS-TRIS propane; pH 7.0 7 % v/v 2-Methyl-2,4-pentanediol, 5 % v/v 2-Methyl-2-propanol, 6% ???PEG 5000
Crystal Properties Matthews coefficient Solvent content 2.33 47.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.819 α = 90 b = 83.819 β = 90 c = 89.044 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 110 CCD Bruker Platinum 135 2014-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.1 24.222 99.9 0.071 10.96 11 19130
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 0.537
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1GZJ 2.1 24.222 1.35 19007 963 99.6 0.2203 0.218 0.2599 0.232
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 13.692 f_angle_d 0.766 f_chiral_restr 0.048 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2371 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling PHASER phasing