5QQC

Crystal Structure of T. cruzi FPPS after initial refinement with no ligand modelled (structure $n)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529380 mM MES, 4 mM ZnSO4, 12.36% w/v PEG MME 550, 11.57% v/v glycerol
Crystal Properties
Matthews coefficientSolvent content
2.346.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.681α = 90
b = 57.681β = 90
c = 396.512γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-10-08SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

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
11.62132.191000.10.1030.0240.9991517.751799
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)
11.621.661002.7342.8310.730.52314.93733

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1YHK1.6266.0948589265099.150.19340.19160.2274RANDOM30.73
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.017
r_dihedral_angle_4_deg19.188
r_dihedral_angle_3_deg14.235
r_dihedral_angle_1_deg5.36
r_mcangle_it3.673
r_mcbond_it2.729
r_mcbond_other2.728
r_angle_refined_deg2.015
r_angle_other_deg1.103
r_chiral_restr0.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.017
r_dihedral_angle_4_deg19.188
r_dihedral_angle_3_deg14.235
r_dihedral_angle_1_deg5.36
r_mcangle_it3.673
r_mcbond_it2.729
r_mcbond_other2.728
r_angle_refined_deg2.015
r_angle_other_deg1.103
r_chiral_restr0.125
r_bond_refined_d0.022
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 Atoms2871
Nucleic Acid Atoms
Solvent Atoms292
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing