4XQR

Crystal structure of unliganded human FPPS at 2.15 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5295.1517% PEG 4000, 8.5% 2-propanol, 15% glycerol, 0.09 M HEPES
Crystal Properties
Matthews coefficientSolvent content
2.7855.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.85α = 90
b = 110.85β = 90
c = 78.08γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002013-02-13MSINGLE 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)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
12.1555.4299.70.08213.99.726862
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)
12.152.2198.90.9912.52.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2F7M2.1555.4225437137099.660.187030.185020.22475RANDOM69.975
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]
-4.34-4.348.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.525
r_dihedral_angle_4_deg19.3
r_dihedral_angle_3_deg16.015
r_long_range_B_refined7.112
r_long_range_B_other7.048
r_dihedral_angle_1_deg6.294
r_scangle_other5.219
r_mcangle_it4.358
r_mcangle_other4.357
r_scbond_other3.558
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.525
r_dihedral_angle_4_deg19.3
r_dihedral_angle_3_deg16.015
r_long_range_B_refined7.112
r_long_range_B_other7.048
r_dihedral_angle_1_deg6.294
r_scangle_other5.219
r_mcangle_it4.358
r_mcangle_other4.357
r_scbond_other3.558
r_scbond_it3.557
r_mcbond_it2.871
r_mcbond_other2.87
r_angle_refined_deg1.75
r_angle_other_deg0.884
r_chiral_restr0.093
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2664
Nucleic Acid Atoms
Solvent Atoms58
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing