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Crystal structure of yeast alpha1,2-mannosyltransferase Kre2p/Mnt1p: ternary complex with GDP/Mn and methyl-alpha-mannoside acceptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S4O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 GDP, manganese chloride, methyl-alpha-mannoside, PEG 2000 MME, HEPES, SODIUM CHLORIDE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.694 α = 90 b = 101.068 β = 98.81 c = 62.036 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 93 IMAGE PLATE RIGAKU RAXIS IV++ MIRRORS 2003-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.01 50 95.1 0.071 0.071 23.9 7.46 50026 50026 31.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.08 93.2 0.316 0.316 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1S4O 2.01 19.96 46610 46610 3280 94.8 0.203 0.203 0.203 0.2127 0.256 0.2638 RANDOM 25.9
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] -0.28 2.25 2.76 -2.48
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_scangle_it 2.67 c_scbond_it 1.96 c_mcangle_it 1.78 c_angle_deg 1.6 c_mcbond_it 1.27 c_improper_angle_d 1 c_bond_d 0.01 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_scangle_it 2.67 c_scbond_it 1.96 c_mcangle_it 1.78 c_angle_deg 1.6 c_mcbond_it 1.27 c_improper_angle_d 1 c_bond_d 0.01 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5657 Nucleic Acid Atoms Solvent Atoms 853 Heterogen Atoms 240
Software Software Software Name Purpose CNS refinement CrystalClear data reduction d*TREK data scaling CNS phasing