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Crystal Structure of Glycosyltransferase from Rickettsia africae ESF-5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6D9T MR-rosetta starting from pdb entry 6d9t
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 287 Rigaku Reagens JCSG+ screen, condtion E1: 1000mM sodium citrate tribasic, 100mM sodium cacodylate / HCl pH 6.5: RiafA.17295.a.B1.PW36512 at 23.9mg/ml: tray: 240851 e1: cryo: 20% EG: puck osj0-7
Crystal Properties Matthews coefficient Solvent content 3.25 62.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.27 α = 90 b = 111.27 β = 90 c = 163.74 γ = 120
Symmetry Space Group P 65 2 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 RAYONIX MX-300 Beryllium Lenses 2013-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.979190 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.9 50 99.8 0.083 0.09 0.999 21.03 7.074 13909 55.775
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.98 100 0.646 0.696 0.908 3.36 7.249
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE MR-rosetta starting from pdb entry 6d9t 2.9 47.49 1.34 13870 1346 99.91 0.1982 0.1941 0.1889 0.2363 0.2325 0 64.67
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.5704 f_angle_d 0.557 f_chiral_restr 0.0442 f_plane_restr 0.0046 f_bond_d 0.0037
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2876 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 4
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MR-Rosetta phasing PHENIX model building Coot model building