6N7Z

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 DROP2950.08 M TrisHCl pH 8.5, 1.6 M Ammonium phosphate, 20% (v/v) glycerol
Crystal Properties
Matthews coefficientSolvent content
2.6753.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.862α = 90
b = 110.862β = 90
c = 75.038γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER PHOTON 1002016-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1LIQUID ANODEBRUKER METALJET1.3418

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
12.5554.2199.90.09614.4615.9815822
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)
12.552.651000.5712.7316.27

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 SYNTHESISTHROUGHOUT4XQR2.5544.631474572697.970.234390.232110.28103RANDOM71.301
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]
-7.03-7.0314.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.271
r_dihedral_angle_4_deg22.395
r_dihedral_angle_3_deg18.333
r_long_range_B_refined7.379
r_long_range_B_other7.372
r_dihedral_angle_1_deg6.89
r_scangle_other2.816
r_mcangle_it2.637
r_mcangle_other2.636
r_scbond_it1.712
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.271
r_dihedral_angle_4_deg22.395
r_dihedral_angle_3_deg18.333
r_long_range_B_refined7.379
r_long_range_B_other7.372
r_dihedral_angle_1_deg6.89
r_scangle_other2.816
r_mcangle_it2.637
r_mcangle_other2.636
r_scbond_it1.712
r_scbond_other1.711
r_mcbond_it1.591
r_mcbond_other1.591
r_angle_refined_deg1.584
r_angle_other_deg1.017
r_chiral_restr0.077
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.001
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 Atoms2619
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
REFMACphasing