6OAH

Crystal structure of human FPPS in complex with an allosteric inhibitor YF-02-78


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4H5C 

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
2.5151.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.33α = 90
b = 111.33β = 90
c = 70γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2019-02-15MSINGLE 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
12.278.7299.50.0660.0690.019119.612.92271548.072
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)
12.22.2498.61.651.7180.4750.481.712.8

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 SYNTHESISTHROUGHOUT4H5C2.278.7221448121599.270.210460.207610.26041RANDOM71.491
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]
-6.19-6.1912.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.736
r_dihedral_angle_3_deg17.72
r_dihedral_angle_4_deg16.418
r_long_range_B_refined7.106
r_long_range_B_other6.968
r_dihedral_angle_1_deg6.692
r_scangle_other4.101
r_mcangle_other3.322
r_mcangle_it3.321
r_scbond_it2.643
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.736
r_dihedral_angle_3_deg17.72
r_dihedral_angle_4_deg16.418
r_long_range_B_refined7.106
r_long_range_B_other6.968
r_dihedral_angle_1_deg6.692
r_scangle_other4.101
r_mcangle_other3.322
r_mcangle_it3.321
r_scbond_it2.643
r_scbond_other2.589
r_mcbond_it2.192
r_mcbond_other2.19
r_angle_refined_deg1.667
r_angle_other_deg1.374
r_chiral_restr0.071
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.002
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 Atoms2716
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing