6N82

Crystal structure of human FPPS in complex with an allosteric inhibitor YF-02037


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52951.36M tri-sodium citrate 15% (v/v) glycerol
Crystal Properties
Matthews coefficientSolvent content
2.7655.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.92α = 90
b = 110.92β = 90
c = 77.53γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2018-06-23MSINGLE 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
1278.4399.80.0430.0450.013125.912.93308046.204
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)
122.04991.2441.2980.3650.8742.412.4

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 SYNTHESISTHROUGHOUT4XQR278.4331318170499.60.173770.172180.20442RANDOM70.04
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]
-3.87-3.877.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.306
r_dihedral_angle_4_deg21.833
r_dihedral_angle_3_deg16.254
r_long_range_B_refined9.129
r_long_range_B_other8.974
r_dihedral_angle_1_deg6.137
r_scangle_other5.226
r_scbond_it3.945
r_mcangle_other3.819
r_mcangle_it3.818
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.306
r_dihedral_angle_4_deg21.833
r_dihedral_angle_3_deg16.254
r_long_range_B_refined9.129
r_long_range_B_other8.974
r_dihedral_angle_1_deg6.137
r_scangle_other5.226
r_scbond_it3.945
r_mcangle_other3.819
r_mcangle_it3.818
r_scbond_other3.789
r_mcbond_it2.689
r_mcbond_other2.678
r_angle_refined_deg1.867
r_angle_other_deg1.136
r_chiral_restr0.088
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.004
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 Atoms2698
Nucleic Acid Atoms
Solvent Atoms115
Heterogen Atoms89

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing