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Crystal Structure of Alpha-1,3-mannosyltransferase MNT2 from Saccharomyces cerevisiae, Mn/GDP-mannose form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Predicted structure model by Alphafold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 PEG 20000
Crystal Properties Matthews coefficient Solvent content 3.05 59.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.849 α = 90 b = 131.189 β = 90 c = 169.552 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 PIXEL DECTRIS EIGER X 16M 2022-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.8 50 99.7 0.988 7.7 6.9 139005
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.97 0.947
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE Predicted structure model by Alphafold 2.8 40.003 72434 3516 99.916 0.215 0.2135 0.2164 0.2508 0.2478 71.951
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] 2.681 3.125 -5.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.078 r_dihedral_angle_3_deg 13.45 r_dihedral_angle_4_deg 9.609 r_lrange_it 7.224 r_lrange_other 7.224 r_dihedral_angle_1_deg 5.745 r_scangle_it 4.616 r_scangle_other 4.615 r_mcangle_it 4.566 r_mcangle_other 4.566
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.078 r_dihedral_angle_3_deg 13.45 r_dihedral_angle_4_deg 9.609 r_lrange_it 7.224 r_lrange_other 7.224 r_dihedral_angle_1_deg 5.745 r_scangle_it 4.616 r_scangle_other 4.615 r_mcangle_it 4.566 r_mcangle_other 4.566 r_scbond_it 2.81 r_scbond_other 2.81 r_mcbond_it 2.765 r_mcbond_other 2.765 r_angle_refined_deg 1.204 r_angle_other_deg 1.061 r_nbd_other 0.208 r_nbd_refined 0.171 r_symmetry_nbd_other 0.162 r_nbtor_refined 0.159 r_symmetry_nbd_refined 0.156 r_xyhbond_nbd_refined 0.137 r_ncsr_local_group_6 0.101 r_ncsr_local_group_4 0.096 r_ncsr_local_group_5 0.094 r_ncsr_local_group_3 0.093 r_symmetry_xyhbond_nbd_refined 0.089 r_ncsr_local_group_2 0.089 r_ncsr_local_group_1 0.087 r_symmetry_nbtor_other 0.071 r_symmetry_xyhbond_nbd_other 0.07 r_chiral_restr 0.04 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16882 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 267
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing