5JV0

Crystal structure of human FPPS in complex with an allosteric inhibitor CL-08-038


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2950.85 M lithium sulfate, 0.425 M ammonium sulfate, 15% glycerol, 0.085 M tri-sodium citrate, pH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.7455.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.54α = 90
b = 111.54β = 90
c = 75.98γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2015-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.441.788.40.06431.912.11715036.381
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4652.40.7132.15.1

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 SYNTHESISTHROUGHOUT4QXS2.441.71625186388.240.179360.176360.23504RANDOM56.403
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]
-3.41-3.416.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.168
r_dihedral_angle_4_deg22.924
r_dihedral_angle_3_deg16.397
r_long_range_B_refined7.672
r_long_range_B_other7.672
r_dihedral_angle_1_deg6.671
r_scangle_other3.665
r_mcangle_other2.492
r_mcangle_it2.49
r_scbond_it2.437
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.168
r_dihedral_angle_4_deg22.924
r_dihedral_angle_3_deg16.397
r_long_range_B_refined7.672
r_long_range_B_other7.672
r_dihedral_angle_1_deg6.671
r_scangle_other3.665
r_mcangle_other2.492
r_mcangle_it2.49
r_scbond_it2.437
r_scbond_other2.437
r_angle_refined_deg2.132
r_mcbond_it1.533
r_mcbond_other1.524
r_angle_other_deg1.191
r_chiral_restr0.116
r_bond_refined_d0.022
r_gen_planes_refined0.009
r_bond_other_d0.003
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 Atoms2701
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing