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Crystal structure of AviGT4, a glycosyltransferase involved in Avilamycin A biosynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IUY PDB ENTRY 2IUY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 18% PEG 3350, 0.2M LI2SO4, 0.1M MES PH6.5
Crystal Properties Matthews coefficient Solvent content 2.2 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.47 α = 89.99 b = 74.37 β = 92.7 c = 90.64 γ = 100.73
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD MARRESEARCH 2005-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 SRS PX10.1
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 2.3 20 96.9 0.09 9.8 2.5 56829 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 2.3 2.42 92.3 0.32 2.6 2.4
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 2IUY 2.3 20 53958 2869 97.1 0.21 0.207 0.2109 0.273 0.2753 RANDOM 40.26
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] -0.98 -0.19 -0.04 0.62 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.087 r_dihedral_angle_4_deg 21.37 r_dihedral_angle_3_deg 18.785 r_dihedral_angle_1_deg 7.529 r_scangle_it 2.112 r_angle_refined_deg 1.704 r_scbond_it 1.479 r_mcangle_it 0.825 r_mcbond_it 0.55 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.087 r_dihedral_angle_4_deg 21.37 r_dihedral_angle_3_deg 18.785 r_dihedral_angle_1_deg 7.529 r_scangle_it 2.112 r_angle_refined_deg 1.704 r_scbond_it 1.479 r_mcangle_it 0.825 r_mcbond_it 0.55 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.287 r_nbd_refined 0.237 r_symmetry_hbond_refined 0.229 r_xyhbond_nbd_refined 0.198 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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 10034 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing