5JV2

Crystal structure of human FPPS in complex with an allosteric inhibitor MIT-01-055


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2951.6 M ammonium phosphate, 20% glycerol, 0.08 M TrisHCl, pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.6954.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.41α = 90
b = 110.41β = 90
c = 76.27γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2016-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

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
12.355.21990.04844.2172133737.923
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)
12.32.3698.80.9722.611.4

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 SYNTHESISTHROUGHOUT4QXS2.355.2120190110698.990.188940.186230.23658RANDOM59.844
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]
-3.17-3.176.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.446
r_dihedral_angle_4_deg18.709
r_dihedral_angle_3_deg16.267
r_long_range_B_refined8.196
r_long_range_B_other8.195
r_dihedral_angle_1_deg6.133
r_scangle_other4.399
r_scbond_it2.809
r_scbond_other2.808
r_mcangle_it2.759
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.446
r_dihedral_angle_4_deg18.709
r_dihedral_angle_3_deg16.267
r_long_range_B_refined8.196
r_long_range_B_other8.195
r_dihedral_angle_1_deg6.133
r_scangle_other4.399
r_scbond_it2.809
r_scbond_other2.808
r_mcangle_it2.759
r_mcangle_other2.759
r_angle_refined_deg2.157
r_mcbond_it1.818
r_mcbond_other1.805
r_angle_other_deg1.179
r_chiral_restr0.122
r_bond_refined_d0.024
r_gen_planes_refined0.011
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 Atoms2602
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing