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Crystal structure of Beta-D-Mannosidase from Dictyoglomus thermophilum.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JE8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 24% PEG400, 0.1 M Na-HEPES pH 7, 200 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.9 57.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.25 α = 90 b = 75.56 β = 92.52 c = 217.88 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 200 PIXEL DECTRIS PILATUS 6M 2015-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 3.08 49.5 98.9 0.185 0.216 0.11 7.3 3.74 71693
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.08 3.14 1.762 2.083 1.093
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2JE8 3.08 49.5 71693 3813 88.15 0.20637 0.20376 0.202 0.25483 0.2509 RANDOM
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] -45.63 7.1 68.52 -22.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.409 r_dihedral_angle_3_deg 18.292 r_dihedral_angle_4_deg 17.068 r_long_range_B_refined 14.368 r_long_range_B_other 14.368 r_mcangle_it 10.407 r_mcangle_other 10.407 r_scangle_other 10.126 r_dihedral_angle_1_deg 9.083 r_mcbond_it 6.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.409 r_dihedral_angle_3_deg 18.292 r_dihedral_angle_4_deg 17.068 r_long_range_B_refined 14.368 r_long_range_B_other 14.368 r_mcangle_it 10.407 r_mcangle_other 10.407 r_scangle_other 10.126 r_dihedral_angle_1_deg 9.083 r_mcbond_it 6.727 r_mcbond_other 6.727 r_scbond_it 6.453 r_scbond_other 6.453 r_angle_refined_deg 1.771 r_angle_other_deg 1.476 r_chiral_restr 0.113 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27200 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction MOLREP phasing Aimless data scaling