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Structure of mouse Golgi alpha-1,2-mannosidase IA reveals the molecular basis for substrate specificity among Class I enzymes (family 47 glycosidases)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 PEG4000, pH 4.5-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.25 44.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.288 α = 90 b = 72.164 β = 90 c = 129.571 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 IMAGE PLATE RIGAKU RAXIS IV MSC Blue Confocal Optics 2002-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-D 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.51 62.5 0.06 10.2 81971 73142 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.63 0.147 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.51 62.5 82108 69386 3689 89.18 0.17174 0.17079 0.1897 0.2005 RANDOM 8.55
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] 0.41 -0.39 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.837 r_sphericity_free 5.32 r_sphericity_bonded 3.069 r_scangle_it 2.587 r_scbond_it 1.664 r_angle_refined_deg 1.382 r_rigid_bond_restr 1.334 r_mcangle_it 1.104 r_angle_other_deg 0.903 r_mcbond_it 0.613
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.837 r_sphericity_free 5.32 r_sphericity_bonded 3.069 r_scangle_it 2.587 r_scbond_it 1.664 r_angle_refined_deg 1.382 r_rigid_bond_restr 1.334 r_mcangle_it 1.104 r_angle_other_deg 0.903 r_mcbond_it 0.613 r_nbd_other 0.234 r_symmetry_vdw_other 0.226 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.185 r_xyhbond_nbd_refined 0.124 r_symmetry_hbond_refined 0.121 r_nbtor_other 0.112 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_xyhbond_nbd_other r_symmetry_hbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3693 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 95
Software Software Software Name Purpose EPMR phasing REFMAC refinement PROTEUM PLUS data reduction