3BD1

Structure of the Cro protein from putative prophage element Xfaso 1 in Xylella fastidiosa strain Ann-1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529816% 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 coefficientSolvent content
2.8356.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.97α = 90
b = 66.97β = 90
c = 54.36γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9002APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.458.0398.60.04813.33.615372623.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4599.70.3863.23.655367

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONACORN (DDM)THROUGHOUTPDB entry 2HIN1.417.065564252945269798.50.1470.1470.182RANDOM18.77
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]
-0.73-0.37-0.731.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.92
r_sphericity_free18.588
r_dihedral_angle_4_deg15.105
r_dihedral_angle_3_deg12.905
r_scangle_it12.145
r_sphericity_bonded9.454
r_scbond_it9.176
r_mcangle_it5.579
r_rigid_bond_restr5.312
r_mcbond_it5.283
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.92
r_sphericity_free18.588
r_dihedral_angle_4_deg15.105
r_dihedral_angle_3_deg12.905
r_scangle_it12.145
r_sphericity_bonded9.454
r_scbond_it9.176
r_mcangle_it5.579
r_rigid_bond_restr5.312
r_mcbond_it5.283
r_dihedral_angle_1_deg4.354
r_mcbond_other3.971
r_angle_other_deg2.7
r_angle_refined_deg1.792
r_symmetry_vdw_other0.333
r_symmetry_vdw_refined0.243
r_nbd_other0.237
r_nbd_refined0.231
r_xyhbond_nbd_refined0.19
r_nbtor_refined0.177
r_symmetry_hbond_refined0.147
r_chiral_restr0.103
r_nbtor_other0.082
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms1441
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms35

Software

Software
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDISPLAYFdata collection
d*TREKdata reduction
ACORNphasing