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Crystal structure of a virus encoded glycosyltransferase in complex with GDP-mannose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 crystallization solution:100mM Tris-HCl pH7.0, 20% w/v PEG3350
soaking solution: 100mM Tris-HCl pH7.0, 20% w/v PEG3350, 10mM GDP-mannose
, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.39 63.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.248 α = 90 b = 243.189 β = 90 c = 67.402 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 CCD MarCCD 300 2009-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.98 APS 23-ID-D
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 2.7 50 98.4 0.091 0.091 19.1 34259 33711
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) 2.74 2.84 86.7 0.566 0.566 2.3
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 FOURIER SYNTHESIS THROUGHOUT 2.73 130.19 34259 31999 1701 98.69 0.25854 0.25687 0.28965 0.2891 RANDOM 31.923
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] 6.07 -1.16 -4.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.643 r_dihedral_angle_3_deg 18.406 r_dihedral_angle_4_deg 17.32 r_dihedral_angle_1_deg 5.047 r_angle_refined_deg 1.06 r_scangle_it 0.867 r_scbond_it 0.511 r_mcangle_it 0.419 r_mcbond_it 0.22 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.643 r_dihedral_angle_3_deg 18.406 r_dihedral_angle_4_deg 17.32 r_dihedral_angle_1_deg 5.047 r_angle_refined_deg 1.06 r_scangle_it 0.867 r_scbond_it 0.511 r_mcangle_it 0.419 r_mcbond_it 0.22 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6202 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 78
Software Software Software Name Purpose Blu-Ice data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing