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Landomycin Glycosyltransferase LanGT2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P6P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 293 1.3 M sodium citrate
0.1 M HEPES/NaOH, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.992 α = 90 b = 75.992 β = 90 c = 214.314 γ = 120
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 PILATUS 6M 2013-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00 SLS X06SA
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 2.16 214.31 100 0.043 40.4 37364 37364 2 2.5
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 2.16 2.28 100 0.49 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 2P6P 2.162 65.81 37364 35420 1859 99.99 0.19975 0.19975 0.19755 0.1973 0.24198 0.2393 RANDOM 46.688
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] 0.42 0.42 0.42 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.737 r_dihedral_angle_3_deg 16.343 r_dihedral_angle_4_deg 16.148 r_dihedral_angle_1_deg 6.041 r_long_range_B_refined 5.518 r_mcangle_it 2.258 r_scbond_it 1.586 r_mcbond_it 1.368 r_angle_refined_deg 1.334 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.737 r_dihedral_angle_3_deg 16.343 r_dihedral_angle_4_deg 16.148 r_dihedral_angle_1_deg 6.041 r_long_range_B_refined 5.518 r_mcangle_it 2.258 r_scbond_it 1.586 r_mcbond_it 1.368 r_angle_refined_deg 1.334 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 5273 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling