5KSX

Crystal structure of human FPPS in complex with an allosteric inhibitor AM-02-072


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5295.150.6 M sodium phosphate, 0.6 M potassium phosphate, 25% glycerol, 0.075 M HEPES, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.6653.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.48α = 90
b = 110.48β = 90
c = 75.2γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2015-05-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.6555.2499.80.0850.99926.712.51400741.62
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.72981.0370.7481.97.7

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 SYNTHESISTHROUGHOUT4XQR2.6555.241326670299.760.174510.170960.24291RANDOM62.585
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]
-3.5-3.56.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.263
r_dihedral_angle_4_deg20.567
r_dihedral_angle_3_deg16.351
r_long_range_B_refined6.508
r_long_range_B_other6.507
r_dihedral_angle_1_deg6.364
r_scangle_other3.978
r_mcangle_it2.706
r_mcangle_other2.705
r_scbond_it2.643
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.263
r_dihedral_angle_4_deg20.567
r_dihedral_angle_3_deg16.351
r_long_range_B_refined6.508
r_long_range_B_other6.507
r_dihedral_angle_1_deg6.364
r_scangle_other3.978
r_mcangle_it2.706
r_mcangle_other2.705
r_scbond_it2.643
r_scbond_other2.642
r_angle_refined_deg2.075
r_mcbond_it1.734
r_mcbond_other1.677
r_angle_other_deg1.174
r_chiral_restr0.105
r_bond_refined_d0.02
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 Atoms2683
Nucleic Acid Atoms
Solvent Atoms76
Heterogen Atoms69

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing