4QXS

Crystal structure of human FPPS in complex with WC01088


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2F7MPDB ENTRY 2F7M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52951.6 M ammonium phosphate, 20% glycerol, 0.08 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.7655.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.65α = 90
b = 110.65β = 90
c = 77.92γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002014-07-08MSINGLE 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
11.955.2199.40.04128.29.7384343843436.5
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)
11.91.9598.61.1772.99.62768

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 2F7M1.955.213635536355202399.270.171450.171450.169520.20649RANDOM59.447
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]
-3.38-3.386.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.531
r_dihedral_angle_4_deg17.022
r_dihedral_angle_3_deg14.84
r_long_range_B_refined8.145
r_long_range_B_other8.144
r_dihedral_angle_1_deg5.891
r_scangle_other5.599
r_mcangle_other4.004
r_mcangle_it4.002
r_scbond_it3.895
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.531
r_dihedral_angle_4_deg17.022
r_dihedral_angle_3_deg14.84
r_long_range_B_refined8.145
r_long_range_B_other8.144
r_dihedral_angle_1_deg5.891
r_scangle_other5.599
r_mcangle_other4.004
r_mcangle_it4.002
r_scbond_it3.895
r_scbond_other3.892
r_mcbond_it2.769
r_mcbond_other2.753
r_angle_refined_deg1.866
r_angle_other_deg0.907
r_chiral_restr0.104
r_bond_refined_d0.02
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2674
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms46

Software

Software
Software NamePurpose
MxDCdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing