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Structure of a Glycosyltransferase in Complex with Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BO6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 293 130 mM (NH)4H2PO4, 22% PEG2000 and 50 mM PIPES pH 7.3
Crystal Properties Matthews coefficient Solvent content 2.9 61.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.84 α = 90 b = 96.64 β = 90 c = 124.78 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE MAR scanner 345 mm plate 2015-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002 1.502
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.15 52.72 100 0.084 0.047 0.997 11.8 4.1 48673
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.22 100 0.604 0.34 0.709 2.3 4.1 4142
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5BO6 2.15 52.72 46200 2407 99.97 0.2 0.1981 0.2352 0.2211 RANDOM 38.139
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] 1.58 -0.07 -1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.725 r_dihedral_angle_4_deg 17.329 r_dihedral_angle_3_deg 16.441 r_dihedral_angle_1_deg 6.303 r_mcangle_it 5.133 r_mcbond_it 3.481 r_mcbond_other 3.472 r_angle_refined_deg 1.89 r_angle_other_deg 1.474 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.725 r_dihedral_angle_4_deg 17.329 r_dihedral_angle_3_deg 16.441 r_dihedral_angle_1_deg 6.303 r_mcangle_it 5.133 r_mcbond_it 3.481 r_mcbond_other 3.472 r_angle_refined_deg 1.89 r_angle_other_deg 1.474 r_chiral_restr 0.107 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d 0.008 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4805 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 289
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing