6N83

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, SITTING DROP2950.08 M TrisHCl ph 8.5, 1.6 M Ammonium phosphate, 20% (v/v) glycerol
Crystal Properties
Matthews coefficientSolvent content
2.7455.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.08α = 90
b = 111.08β = 90
c = 76.73γ = 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
12111.0899.30.0430.0450.0130.99925.7133284948.823
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)
122.03991.3751.4310.3920.8612.213.1

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 SYNTHESISTHROUGHOUT4XQR278.6731095169699.340.188020.186330.21745RANDOM75.052
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]
-4.86-4.869.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.649
r_dihedral_angle_4_deg22.759
r_dihedral_angle_3_deg16.604
r_long_range_B_refined8.801
r_long_range_B_other8.656
r_dihedral_angle_1_deg6.693
r_scangle_other4.999
r_mcangle_it3.87
r_mcangle_other3.869
r_scbond_it3.562
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.649
r_dihedral_angle_4_deg22.759
r_dihedral_angle_3_deg16.604
r_long_range_B_refined8.801
r_long_range_B_other8.656
r_dihedral_angle_1_deg6.693
r_scangle_other4.999
r_mcangle_it3.87
r_mcangle_other3.869
r_scbond_it3.562
r_scbond_other3.415
r_mcbond_it2.599
r_mcbond_other2.597
r_angle_refined_deg1.669
r_angle_other_deg1.052
r_chiral_restr0.084
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.001
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 Atoms2694
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing