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Dolichyl phosphate mannose synthase in complex with donor (GDP-Man) and traces of acceptor (Dol55P) and product (Dol55P-Man)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Wildtype PfDPMS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 0.2 M potassium chloride, 0.1 M trisodium citrate (pH 5.5), 37% (v/v) pentaerythritol propoxylate (5/4 PO/OH), 50 mM Hepes (pH 7.5), 150 mM NaCl, 10% (v/v) glycerol, 0.05% LDAO, 5 mM GDP-mannose, 5 mM MgCl2, 0.25 mM C55 dolichyl phosphate
Crystal Properties Matthews coefficient Solvent content 3.7 66.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.8 α = 90 b = 145.25 β = 90 c = 99.02 γ = 90
Symmetry Space Group C 2 2 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 PILATUS3 6M 2016-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.9 43.9 99.6 0.133 0.999 15.4 13.2 14327 89.4
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 2.9 3 99.3 0.715 13.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.9 43.9 1.36 14315 1442 99.55 0.2429 0.2369 0.2488 0.3006 0.3031
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.17 f_angle_d 1.183 f_chiral_restr 0.058 f_plane_restr 0.015 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2771 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 88
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing