2F8Z

Crystal structure of human FPPS in complex with zoledronate and isopentenyl diphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2F8CPDB ENTRY 2F8C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.72921.2M sodium potassium phosphate, 25% glycerol, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.5752.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.155α = 90
b = 112.155β = 90
c = 65.725γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDMARRESEARCH2004-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.00033SLSX06SA

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
12.610099.90.0728.87.7132481324862.5
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)
12.62.6999.80.4811282

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 2F8C2.656.711321213212135899.80.2260.2260.220.28RANDOM59.9
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]
-20.79-20.7941.58
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d21.3
x_scangle_it7.36
x_scbond_it5.31
x_mcangle_it5.17
x_mcbond_it3.37
x_angle_d1.2
x_improper_angle_d0.74
x_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2806
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms33

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNXrefinement
CNXphasing