6OS6

Crystal structure of CymD prenyltransferase complexed with L-tryptophan and DMSPP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5JXMAuthor used SWISS-MODEL server to generate a phasing model based on the protein sequence. SWISS-MODEL produced a phasing model based on PDB Entry 5JXM. Author used the polyALA version of the model for phasing.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2941% (w/v) tryptone, 0.05 M HEPES-Na (pH 7.0), 12% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.6253.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.446α = 90
b = 129.446β = 90
c = 49.777γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-20.97932NSLS-II17-ID-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.3329.1299.80.070.0750.0270.999157.59502113.86
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.331.3697.30.6850.7390.2750.8067

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTAuthor used SWISS-MODEL server to generate a phasing model based on the protein sequence. SWISS-MODEL produced a phasing model based on PDB Entry 5JXM. Author used the polyALA version of the model for phasing.1.3329.1181.3695019199399.810.16650.16620.180918.9029
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2772
Nucleic Acid Atoms
Solvent Atoms411
Heterogen Atoms66

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing