4NFK

Crystal structure of human FPPS in complex with nickel, JDS05120, and sulfate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52950.85M lithium sulfate, 0.01M nickel chloride, 15% glycerol, 0.09M TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.4449.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.94α = 90
b = 110.94β = 90
c = 68.46γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002013-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

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
11.8551.5898.70.04925.89.8364453644523.7
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)
11.851.997.70.474.79.62615

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 4H5D1.8551.583400834008179597.140.15340.15340.151840.18195RANDOM39.154
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]
-2.95-2.955.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.203
r_dihedral_angle_4_deg20.71
r_dihedral_angle_3_deg13.808
r_long_range_B_refined6.629
r_long_range_B_other6.628
r_dihedral_angle_1_deg5.288
r_scangle_other4.6
r_scbond_other3.109
r_scbond_it3.105
r_mcangle_it2.426
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.203
r_dihedral_angle_4_deg20.71
r_dihedral_angle_3_deg13.808
r_long_range_B_refined6.629
r_long_range_B_other6.628
r_dihedral_angle_1_deg5.288
r_scangle_other4.6
r_scbond_other3.109
r_scbond_it3.105
r_mcangle_it2.426
r_mcangle_other2.426
r_angle_refined_deg1.837
r_mcbond_it1.836
r_mcbond_other1.826
r_angle_other_deg0.939
r_chiral_restr0.125
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2745
Nucleic Acid Atoms
Solvent Atoms220
Heterogen Atoms34

Software

Software
Software NamePurpose
MxDCdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing