4JB7

1.42 Angstrom resolution crystal structure of accessory colonization factor AcfC (acfC) in complex with D-aspartic acid


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9295Protein: 7.3 mg/mL in 10 mM Tris-HCl, pH 8.0, 0.25 M NaCl 5 mM BME. Crystallization: PACT Suite D6(#42): 0.1 M MMT buffer pH 9.0 25 % (w/v) PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.9938.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.343α = 90
b = 72.343β = 90
c = 87.883γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBe-Lenses2013-02-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
11.42301000.08745.479.54477244772-3
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)
11.421.441000.6153.829.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.4227.934234342343224999.950.126670.125890.14148RANDOM14.643
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]
-0.03-0.030.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.762
r_dihedral_angle_4_deg15.747
r_dihedral_angle_3_deg10.721
r_dihedral_angle_1_deg4.646
r_scangle_it4.06
r_scbond_it2.635
r_mcangle_it1.705
r_angle_refined_deg1.489
r_mcbond_it1.036
r_angle_other_deg0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.762
r_dihedral_angle_4_deg15.747
r_dihedral_angle_3_deg10.721
r_dihedral_angle_1_deg4.646
r_scangle_it4.06
r_scbond_it2.635
r_mcangle_it1.705
r_angle_refined_deg1.489
r_mcbond_it1.036
r_angle_other_deg0.94
r_mcbond_other0.37
r_chiral_restr0.099
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1827
Nucleic Acid Atoms
Solvent Atoms365
Heterogen Atoms37

Software

Software
Software NamePurpose
Blu-Icedata collection
MLPHAREphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling