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Structure of the Cro protein from putative prophage element Xfaso 1 in Xylella fastidiosa strain Ann-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HIN PDB entry 2HIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 16% glycerol, 1.5 M ammonium sulfate, 0.1 M Tris, 1 mM TCEP-hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.83 56.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.97 α = 90 b = 66.97 β = 90 c = 54.36 γ = 120
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 2005-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9002 APS 14-BM-C
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 1.4 58.03 98.6 0.048 13.3 3.61 53726 23.5
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 1.4 1.45 99.7 0.386 3.2 3.65 5367
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 ACORN (DDM) THROUGHOUT PDB entry 2HIN 1.4 17.06 55642 52945 2697 98.5 0.147 0.147 0.1563 0.182 0.1906 RANDOM 18.77
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] -0.73 -0.37 -0.73 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.92 r_sphericity_free 18.588 r_dihedral_angle_4_deg 15.105 r_dihedral_angle_3_deg 12.905 r_scangle_it 12.145 r_sphericity_bonded 9.454 r_scbond_it 9.176 r_mcangle_it 5.579 r_rigid_bond_restr 5.312 r_mcbond_it 5.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.92 r_sphericity_free 18.588 r_dihedral_angle_4_deg 15.105 r_dihedral_angle_3_deg 12.905 r_scangle_it 12.145 r_sphericity_bonded 9.454 r_scbond_it 9.176 r_mcangle_it 5.579 r_rigid_bond_restr 5.312 r_mcbond_it 5.283 r_dihedral_angle_1_deg 4.354 r_mcbond_other 3.971 r_angle_other_deg 2.7 r_angle_refined_deg 1.792 r_symmetry_vdw_other 0.333 r_symmetry_vdw_refined 0.243 r_nbd_other 0.237 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.177 r_symmetry_hbond_refined 0.147 r_chiral_restr 0.103 r_nbtor_other 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1441 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 35
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction XDISPLAYF data collection d*TREK data reduction ACORN phasing