☰ Navigation Tabs
Crystal structure of GH family 81 beta-1,3-glucanase from Rhizomucr miehei complexed with laminarihexaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K3A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 laminarihexaose (G6) was added to the protein solution at a final concentration of 1%(w/v). The complex crystals were obtained in a reservoir solution containing 24%(w/v) PEG4000, 80 mM Tris-HCl (pH 8.5), and 6%(v/v) MPD
Crystal Properties Matthews coefficient Solvent content 1.94 36.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.7 α = 90 b = 99.02 β = 111.35 c = 138.43 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 MAR CCD 130 mm 2014-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1000 Photon Factory BL-1A
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 2.7 50 99.55 0.102 10.37 17 74950
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 2.7 2.94 99.16 0.638 2.36
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 4k3a 2.7 29.73 1.36 74932 2005 99.53 0.1777 0.1762 0.1827 0.2322 0.2278
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 13.738 f_angle_d 1.394 f_chiral_restr 0.092 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22004 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 583
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing