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Selenomethionine derivative of the GH99 endo-alpha-mannosidase from Bacteroides thetaiotaomicron
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.25 M NH4CL, 20% W/V PEG 3350, 0.1 M MES PH 6.5, 5 MM TCEP
Crystal Properties Matthews coefficient Solvent content 2.4 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.721 α = 103.45 b = 60.002 β = 102.59 c = 78.666 γ = 98.59
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 MARRESEARCH MIRRORS 2009-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24
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 1.7 50 95.8 0.06 14.4 3.7 81218 2 19.2
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 1.7 1.76 91.8 0.48 4.9 3.5
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 SAD THROUGHOUT NONE 1.69 73.82 81218 4267 93.59 0.17676 0.17516 0.1779 0.20756 0.2094 RANDOM 21.241
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] 1.09 -1.09 0.55 -0.28 -0.42 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.237 r_dihedral_angle_4_deg 15.481 r_dihedral_angle_3_deg 12.289 r_dihedral_angle_1_deg 5.876 r_angle_refined_deg 1.23 r_nbtor_refined 0.313 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.198 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.237 r_dihedral_angle_4_deg 15.481 r_dihedral_angle_3_deg 12.289 r_dihedral_angle_1_deg 5.876 r_angle_refined_deg 1.23 r_nbtor_refined 0.313 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.198 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.105 r_chiral_restr 0.09 r_mcangle_it 0.016 r_bond_refined_d 0.01 r_mcbond_it 0.01 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5410 Nucleic Acid Atoms Solvent Atoms 652 Heterogen Atoms 48
Software Software Software Name Purpose HKL-2000 data reduction SCALEPACK data scaling SHELX phasing ARP/wARP phasing REFMAC refinement