5JUZ

Crystal structure of human FPPS in complex with an allosteric inhibitor CL-06-057


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2950.6 M sodium phosphate, 0.6 M potassium phosphate, 25% glycerol, 0.075 M HEPES, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.7455.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.9α = 90
b = 110.9β = 90
c = 77γ = 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
12.478.4299.80.09814.19.31930446.933
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)
12.42.4699.40.9312.39.4

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 SYNTHESISTHROUGHOUT4QXS2.478.421832295199.750.182850.18050.22718RANDOM64.524
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]
-2.84-2.845.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.485
r_dihedral_angle_4_deg22.427
r_dihedral_angle_3_deg15.556
r_long_range_B_refined6.675
r_long_range_B_other6.674
r_dihedral_angle_1_deg6.472
r_scangle_other3.923
r_mcangle_it2.986
r_mcangle_other2.985
r_scbond_it2.515
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.485
r_dihedral_angle_4_deg22.427
r_dihedral_angle_3_deg15.556
r_long_range_B_refined6.675
r_long_range_B_other6.674
r_dihedral_angle_1_deg6.472
r_scangle_other3.923
r_mcangle_it2.986
r_mcangle_other2.985
r_scbond_it2.515
r_scbond_other2.515
r_angle_refined_deg2.135
r_mcbond_it1.875
r_mcbond_other1.87
r_angle_other_deg1.168
r_chiral_restr0.113
r_bond_refined_d0.023
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 Atoms2610
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing