4LFV

Crystal structure of human FPPS in complex with YS0470 and two molecules of inorganic phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4H5DPDB ENTRY 4H5D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5295.1530% PEG400, 0.2 M magnesium chloride, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K
Crystal Properties
Matthews coefficientSolvent content
2.3948.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.02α = 90
b = 111.02β = 90
c = 67.04γ = 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
1267.0499.70.0728.814.3288442876224.5
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)
122.0598.80.4987.414.32083

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 4H5D251.032713427134145499.280.17860.17860.176460.21791RANDOM34.973
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]
-2.94-2.945.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.488
r_dihedral_angle_4_deg18.769
r_dihedral_angle_3_deg14.585
r_long_range_B_refined7.075
r_long_range_B_other7.049
r_scangle_other5.745
r_dihedral_angle_1_deg5.47
r_scbond_it3.978
r_scbond_other3.971
r_mcangle_it3.836
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.488
r_dihedral_angle_4_deg18.769
r_dihedral_angle_3_deg14.585
r_long_range_B_refined7.075
r_long_range_B_other7.049
r_scangle_other5.745
r_dihedral_angle_1_deg5.47
r_scbond_it3.978
r_scbond_other3.971
r_mcangle_it3.836
r_mcangle_other3.835
r_mcbond_it3.09
r_mcbond_other3.081
r_angle_refined_deg1.923
r_angle_other_deg0.895
r_chiral_restr0.12
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2728
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms40

Software

Software
Software NamePurpose
MxDCdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing