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Crystal structure of the glycosyltransferase SnogD from Streptomyces nogalater
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AMB PDB ENTRY 4AMB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.7 16 % (W/V) PEG 3350, 0.2 M MGCL2, 0.1 M BISTRIS PH 5.7
Crystal Properties Matthews coefficient Solvent content 2.51 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.676 α = 90 b = 179.798 β = 90 c = 70.246 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.59 48.3 96.2 0.06 15.2 3 26051 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 2.59 2.73 82.4 0.35 2 2.1
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 4AMB 2.59 60 24729 1300 96.16 0.22177 0.22063 0.2173 0.24258 0.2377 RANDOM 45.95
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] -0.75 -0.15 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.931 r_dihedral_angle_4_deg 22.072 r_dihedral_angle_3_deg 18.761 r_dihedral_angle_1_deg 5.201 r_angle_other_deg 1.495 r_angle_refined_deg 1.321 r_chiral_restr 0.061 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.931 r_dihedral_angle_4_deg 22.072 r_dihedral_angle_3_deg 18.761 r_dihedral_angle_1_deg 5.201 r_angle_other_deg 1.495 r_angle_refined_deg 1.321 r_chiral_restr 0.061 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.003 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 5362 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing