☰ Navigation Tabs
Crystal structure of elaiophylin glycosyltransferase in complex with TDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YP3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.2 293 22% polyethylene glycol 3350, 0.15 M DL-Malic pH 7.2, 25% propylene glycol
Crystal Properties Matthews coefficient Solvent content 3.13 60.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.21 α = 90 b = 106.21 β = 90 c = 215.6 γ = 90
Symmetry Space Group P 41 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 315 2014-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97915 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.33 95.28 95.1 0.214 0.219 0.043 0.997 10.2 24.4 50754
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.33 2.41 98.3 2.612 2.674 0.547 0.554 22
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 7YP3 2.33 75.21 48260 2396 94.6 0.2175 0.2154 0.2223 0.2591 0.2648 RANDOM 49.41
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] -0.82 -0.82 1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.333 r_dihedral_angle_3_deg 16.733 r_dihedral_angle_1_deg 7.843 r_angle_refined_deg 1.358 r_angle_other_deg 0.454 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6568 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing