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Crystal structure of beta-mannanase from Streptomyces thermolilacinus with mannohexaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WSU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.1M sodium malonate pH 7.0, 0.1M HEPES pH 7.0, 0.5%(v/v) Jeffamine(R) ED-2001 pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.32 46.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.709 α = 90 b = 100.706 β = 90 c = 104.737 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 ADSC QUANTUM 270 2014-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.45 48.7 95.4 0.097 0.11 12.29 4.56 117826 -3 9.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.54 75 0.591 0.71 1.87
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 FOURIER SYNTHESIS FREE R-VALUE 3WSU 1.5 46.462 1.34 109429 2172 97.99 0.1464 0.1458 0.1475 0.1727 0.1737
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 14.063 f_angle_d 1.398 f_chiral_restr 0.072 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4577 Nucleic Acid Atoms Solvent Atoms 795 Heterogen Atoms 238
Software Software Software Name Purpose PHENIX refinement XDS data reduction PDB_EXTRACT data extraction XDS data scaling PHENIX phasing