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Crystal structure of glycosyltransferase VinC involved in the biosynthesis of vicenistatin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 20%(W/V) PEG 3350, MGCL2, TRIS, HCL, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.43 49.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.205 α = 90 b = 130.392 β = 90 c = 140.107 γ = 90
Symmetry Space Group I 2 2 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 RIGAKU JUPITER 210 2006-06-30 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0, 0.97906, 0.97938, 0.96415 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 43.98 98.5 61121 60204
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 91.2
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 (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 MAD THROUGHOUT 2 40.21 57136 57136 3053 98.4 0.205 0.205 0.202 0.2026 0.253 0.2507 RANDOM 35.66
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.642 r_dihedral_angle_4_deg 21.971 r_dihedral_angle_3_deg 18.635 r_dihedral_angle_1_deg 6.696 r_scangle_it 4.718 r_scbond_it 3.191 r_mcangle_it 2.003 r_angle_refined_deg 1.977 r_mcbond_it 1.193 r_chiral_restr 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.642 r_dihedral_angle_4_deg 21.971 r_dihedral_angle_3_deg 18.635 r_dihedral_angle_1_deg 6.696 r_scangle_it 4.718 r_scbond_it 3.191 r_mcangle_it 2.003 r_angle_refined_deg 1.977 r_mcbond_it 1.193 r_chiral_restr 0.136 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 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 6211 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 1
Software Software Software Name Purpose BSS data collection SOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling