5JV1

Crystal structure of human FPPS in complex with an allosteric inhibitor CL-08-066


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29525.5% PEG 8000, 0.17 M sodium acetate, 15% glycerol, 0.085 M sodium cacodylate, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.7254.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.05α = 90
b = 111.05β = 90
c = 76.2γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002016-04-21MSINGLE 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)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
12.349.6699.50.0621.39.62164647.783
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)
12.32.3698.40.9823.19.6

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4QXS2.349.6620478112399.380.183760.181060.23153RANDOM68.78
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]
-3.38-3.386.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.898
r_dihedral_angle_4_deg16.441
r_dihedral_angle_3_deg15.321
r_long_range_B_refined7.75
r_long_range_B_other7.749
r_dihedral_angle_1_deg6.76
r_scangle_other4.873
r_mcangle_it3.485
r_mcangle_other3.485
r_scbond_it3.374
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.898
r_dihedral_angle_4_deg16.441
r_dihedral_angle_3_deg15.321
r_long_range_B_refined7.75
r_long_range_B_other7.749
r_dihedral_angle_1_deg6.76
r_scangle_other4.873
r_mcangle_it3.485
r_mcangle_other3.485
r_scbond_it3.374
r_scbond_other3.373
r_mcbond_it2.319
r_mcbond_other2.297
r_angle_refined_deg2.136
r_angle_other_deg1.16
r_chiral_restr0.125
r_bond_refined_d0.023
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.002
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 Atoms2635
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing