4LPG

Crystal structure of human FPPS in complex with CL01131


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5295.1517% PEG10000, 6.8% ethylene glycol, 15% glycerol, 0.085 M HEPES, microseeding (see primary citation for details), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K
Crystal Properties
Matthews coefficientSolvent content
2.7455.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.87α = 90
b = 110.87β = 90
c = 77.03γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002012-09-25MSINGLE 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
12.3549.5899.70.04436.714.4206342057349.8
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)
12.352.41980.5275.414.41483

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 2F7M2.3549.581940619406104799.470.183990.183990.181610.22962RANDOM71.347
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]
-3.75-3.757.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.142
r_dihedral_angle_4_deg19.27
r_dihedral_angle_3_deg15.489
r_long_range_B_refined7.035
r_long_range_B_other7.034
r_dihedral_angle_1_deg5.594
r_scangle_other5.048
r_mcangle_it3.703
r_mcangle_other3.702
r_scbond_it3.406
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.142
r_dihedral_angle_4_deg19.27
r_dihedral_angle_3_deg15.489
r_long_range_B_refined7.035
r_long_range_B_other7.034
r_dihedral_angle_1_deg5.594
r_scangle_other5.048
r_mcangle_it3.703
r_mcangle_other3.702
r_scbond_it3.406
r_scbond_other3.405
r_mcbond_it2.479
r_mcbond_other2.478
r_angle_refined_deg1.752
r_angle_other_deg0.847
r_chiral_restr0.093
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2666
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms31

Software

Software
Software NamePurpose
MxDCdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing