7MDF

Full-length S95A ClbP bound to N-acyl-D-asparagine analog


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7MDE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE295Precipitant composition: 1 part 0.1M imidazole pH 7.8, 10% (v/v) PEG 400, 150 mM Li2SO4, 5.5 mM (4-(4-bromophenyl)butanoyl)-D-asparagine plus 3.5 parts 0.1M tris pH 7.4, 28%(v/v) PEG400, 100 mM Li2SO4, 1.2% (w/v) myo-inositol
2LIPIDIC CUBIC PHASE295Precipitant composition: 1 part 0.1M imidazole pH 7.8, 10% (v/v) PEG 400, 150 mM Li2SO4, 5.5 mM (4-(4-bromophenyl)butanoyl)-D-asparagine plus 3.5 parts 0.1M tris pH 7.4, 28%(v/v) PEG400, 100 mM Li2SO4, 1.2% (w/v) myo-inositol
Crystal Properties
Matthews coefficientSolvent content
3.8868.26
3.8868.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.686α = 90
b = 96.686β = 90
c = 182.736γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.92020APS24-ID-C

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
12.346.7499.810.3620.37310.089170.9978.8917.23926833.75
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)
12.32.38299.632.7812.8720.70950.6971.3215.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7MDE2.346.7439236196499.810.19140.21957.39
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.708
f_angle_d0.8938
f_chiral_restr0.0514
f_plane_restr0.0079
f_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3394
Nucleic Acid Atoms
Solvent Atoms309
Heterogen Atoms195

Software

Software
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing