4DEM

Crystal structure of human FPPS in complex with YS_04_70


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3N46PDB ENTRY 3N46

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.629530% PEG 300, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.4349.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.23α = 90
b = 111.23β = 90
c = 67.724γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDRAYONIX MX-3002011-10-13MSINGLE 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)R Sym 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
11.855099.90.0480.04850.414.33688136881
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.881000.3910.3918141816

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3N461.85503486634866183799.410.175450.175450.174090.20176RANDOM26.781
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]
-1.72-1.723.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.486
r_dihedral_angle_4_deg19.371
r_dihedral_angle_3_deg13.823
r_scangle_it5.549
r_dihedral_angle_1_deg4.945
r_scbond_it3.495
r_mcangle_it2.342
r_angle_refined_deg1.749
r_mcbond_it1.381
r_angle_other_deg1.111
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.486
r_dihedral_angle_4_deg19.371
r_dihedral_angle_3_deg13.823
r_scangle_it5.549
r_dihedral_angle_1_deg4.945
r_scbond_it3.495
r_mcangle_it2.342
r_angle_refined_deg1.749
r_mcbond_it1.381
r_angle_other_deg1.111
r_mcbond_other0.425
r_chiral_restr0.129
r_bond_refined_d0.026
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2742
Nucleic Acid Atoms
Solvent Atoms221
Heterogen Atoms29

Software

Software
Software NamePurpose
MxDCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling