7AG5

Structure of the Laspartomycin C double mutant G4D D-allo-Thr9D-Dap in complex with Geranyl phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5O0Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52910.2 M sodium formate, 40% MPD
Crystal Properties
Matthews coefficientSolvent content
2.448.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.428α = 90
b = 40.428β = 90
c = 31.033γ = 120
Symmetry
Space GroupP 6 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-05-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9159DiamondI04-1

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
11.03135.01292.20.1850.1930.0540.997811.76321
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)
11.0311.11653.11.5841.6640.5040.7261.510.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT5O0Z1.0435.01601129982.660.12150.12040.1432RANDOM16.751
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]
0.690.350.69-2.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg67.91
r_dihedral_angle_2_deg24.766
r_dihedral_angle_3_deg12.913
r_rigid_bond_restr2.465
r_angle_refined_deg1.721
r_angle_other_deg0.662
r_chiral_restr0.109
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg67.91
r_dihedral_angle_2_deg24.766
r_dihedral_angle_3_deg12.913
r_rigid_bond_restr2.465
r_angle_refined_deg1.721
r_angle_other_deg0.662
r_chiral_restr0.109
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms91
Nucleic Acid Atoms
Solvent Atoms19
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
Aimlessdata scaling
STARANISOdata scaling
DIALSdata reduction