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Crystal Structure of BepC protein (VirB-translocated Bartonella effector protein) with bound AMPPNP from Bartonella tribocorum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N67
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 at 22.75mg/ml, incubated with 8mM each MgCl2 and AMPPNP, then 1:1 with Morpheus(H2): 10% PEG-8000, 20% ethylene glycol, 0.1M MES/imidazole, pH=6.5, 0.02M each sodium L-glutamate, DL-alanine, glycine, DL-lysine, DL-serine
Crystal Properties Matthews coefficient Solvent content 2.38 48.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.33 α = 90 b = 92.02 β = 90 c = 45.84 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 RIGAKU SATURN 944+ 2014-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.7 50 99.2 0.05 0.056 20.88 4.5 28113 -3 15.95
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 92.1 0.465 0.606 2.1 2
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 4N67 1.7 46.01 1.34 28113 1384 99.22 0.1653 0.1639 0.1658 0.1929 0.1943 Random selection 21.5511
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 12.89 f_angle_d 1.011 f_chiral_restr 0.039 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1640 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 45
Software Software Software Name Purpose XDS data reduction StructureStudio data collection PHENIX refinement PDB_EXTRACT data extraction XSCALE data scaling PHASER phasing ARP model building