6PAE

Dickeya chrysanthemi complex with L-Asp at pH 5.6


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6298see Miller et al., FEBS Letters, 1993, 328, 275-279
Crystal Properties
Matthews coefficientSolvent content
2.1743.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.159α = 90
b = 90.4β = 91.88
c = 127.359γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER R 4MMultilayer X-ray mirrors VariMax HF2017-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
11.5993085.80.05515.12.92136750
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)
11.5991.6681.60.335

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.630133097336885.410.13840.13740.1757RANDOM19.269
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]
1.150.05-0.48-0.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.72
r_sphericity_free26.841
r_dihedral_angle_4_deg16.06
r_dihedral_angle_3_deg13.65
r_sphericity_bonded11.639
r_dihedral_angle_1_deg6.257
r_rigid_bond_restr5.646
r_angle_refined_deg1.981
r_angle_other_deg1.064
r_chiral_restr0.123
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.72
r_sphericity_free26.841
r_dihedral_angle_4_deg16.06
r_dihedral_angle_3_deg13.65
r_sphericity_bonded11.639
r_dihedral_angle_1_deg6.257
r_rigid_bond_restr5.646
r_angle_refined_deg1.981
r_angle_other_deg1.064
r_chiral_restr0.123
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9465
Nucleic Acid Atoms
Solvent Atoms1405
Heterogen Atoms58

Software

Software
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction