6OAG

Crystal structure of human FPPS in complex with an allosteric inhibitor YF-02-82


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52950.075 M HEPES, 0.6 M potassium phosphate, 0.6 M sodium phosphate, 25% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.7655.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.35α = 90
b = 111.35β = 90
c = 76.86γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2019-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-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
12.376.8699.60.0670.0690.02118.812.72195155.395
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)
12.32.3497.31.6311.7070.4960.7971.711.5

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 SYNTHESISTHROUGHOUT4XQR2.355.7420856104799.350.195690.19340.24145RANDOM80.074
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]
-4.41-4.418.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.838
r_dihedral_angle_4_deg18.8
r_dihedral_angle_3_deg16.492
r_long_range_B_refined10.009
r_long_range_B_other9.933
r_dihedral_angle_1_deg6.8
r_scangle_other4.18
r_mcangle_it3.473
r_mcangle_other3.472
r_scbond_it2.621
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.838
r_dihedral_angle_4_deg18.8
r_dihedral_angle_3_deg16.492
r_long_range_B_refined10.009
r_long_range_B_other9.933
r_dihedral_angle_1_deg6.8
r_scangle_other4.18
r_mcangle_it3.473
r_mcangle_other3.472
r_scbond_it2.621
r_scbond_other2.607
r_mcbond_it2.251
r_mcbond_other2.251
r_angle_refined_deg1.685
r_angle_other_deg1.422
r_chiral_restr0.068
r_bond_refined_d0.018
r_bond_other_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.004
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2700
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing