4L2X

Crystal structure of human FPPS in complex with magnesium, CL02134, and inorganic pyrophosphate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5295.1516% PEG8000, 20% glycerol, 0.16 M magnesium acetate, 0.08 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K
Crystal Properties
Matthews coefficientSolvent content
2.4750.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.34α = 90
b = 111.34β = 90
c = 68.77γ = 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
12.555098.30.052249.481462714376
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)
12.552.6293.80.3826.079.521069

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 4H5D2.5535.23133941339470496.830.203550.203550.200830.257RANDOM61.961
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]
-6.17-6.1712.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.461
r_dihedral_angle_4_deg19.066
r_dihedral_angle_3_deg15.073
r_dihedral_angle_1_deg6.18
r_angle_refined_deg1.697
r_angle_other_deg0.851
r_chiral_restr0.08
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.461
r_dihedral_angle_4_deg19.066
r_dihedral_angle_3_deg15.073
r_dihedral_angle_1_deg6.18
r_angle_refined_deg1.697
r_angle_other_deg0.851
r_chiral_restr0.08
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2687
Nucleic Acid Atoms
Solvent Atoms15
Heterogen Atoms40

Software

Software
Software NamePurpose
MxDCdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing