4H5E

Crystal structure of human FPPS in ternary complex with YS0470 and isopentenyl pyrophosphate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.629530% PEG 300, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal Properties
Matthews coefficientSolvent content
2.3547.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.239α = 90
b = 111.239β = 90
c = 65.645γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2011-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
12.04501000.06247.727.32648626486
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)
12.042.091000.5066.926.21289

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 SYNTHESISTHROUGHOUT4DEM2.04502484924849131698.20.188050.188050.185730.23334RANDOM44.763
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]
-2.55-2.555.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.682
r_dihedral_angle_4_deg16.471
r_dihedral_angle_3_deg15.098
r_dihedral_angle_1_deg5.489
r_angle_refined_deg1.991
r_chiral_restr0.204
r_bond_refined_d0.02
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2716
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms43

Software

Software
Software NamePurpose
StructureStudiodata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing