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DISSECTION OF MANNOSYLGLYCERATE SYNTHASE: AN ARCHETYPAL MANNOSYLTRANSFERASE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BO6 PDB ENTRY 2BO6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 10 MM NACL, 0.1 M SODIUM ACETATE TRIHYDRATE, PH 4.6, 15% (V/V) MPD
Crystal Properties Matthews coefficient Solvent content 4.2 70.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 405.094 α = 90 b = 161.43 β = 90 c = 108.708 γ = 90
Symmetry Space Group P 21 21 2
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 ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.8 40 98 0.1 14.5 5.3 175257 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 2.8 2.95 99 0.48 4 4.8
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 PDB ENTRY 2BO6 2.8 74.12 162631 8687 97.4 0.196 0.195 0.2867 0.216 0.2978 RANDOM 58.27
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] 0.91 -0.38 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.076 r_dihedral_angle_3_deg 19.53 r_dihedral_angle_4_deg 19.419 r_dihedral_angle_1_deg 6.436 r_scangle_it 2.453 r_angle_refined_deg 1.914 r_scbond_it 1.564 r_mcangle_it 1.016 r_mcbond_it 0.589 r_symmetry_vdw_refined 0.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.076 r_dihedral_angle_3_deg 19.53 r_dihedral_angle_4_deg 19.419 r_dihedral_angle_1_deg 6.436 r_scangle_it 2.453 r_angle_refined_deg 1.914 r_scbond_it 1.564 r_mcangle_it 1.016 r_mcbond_it 0.589 r_symmetry_vdw_refined 0.476 r_symmetry_hbond_refined 0.376 r_nbtor_refined 0.328 r_nbd_refined 0.241 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.143 r_bond_refined_d 0.023 r_gen_planes_refined 0.007 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_other 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 31380 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 410
Software Software Software Name Purpose REFMAC refinement HKL data reduction HKL data scaling MOLREP phasing