4UMJ

Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01, with bound ibandronic acid molecules.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
180.2 M MGCL2, 20% PEG6000, 0.1 M TRIS CL PH 8
Crystal Properties
Matthews coefficientSolvent content
2.449

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.31α = 90
b = 98.55β = 90
c = 131.32γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002011-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRFESRFID14-4

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
11.8565.6798.80.17.94.3469252
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)
11.851.9594.50.531.82.9

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 DIFFRACTIONOTHERTHROUGHOUTNONE1.8565.6644413236598.480.201780.199640.24269RANDOM25.98
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]
0.96-0.73-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.673
r_dihedral_angle_4_deg20.992
r_dihedral_angle_3_deg13.014
r_dihedral_angle_1_deg5.321
r_scbond_it3.228
r_mcangle_it2.883
r_mcbond_it2.038
r_mcbond_other2.038
r_angle_refined_deg1.764
r_angle_other_deg1.661
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.673
r_dihedral_angle_4_deg20.992
r_dihedral_angle_3_deg13.014
r_dihedral_angle_1_deg5.321
r_scbond_it3.228
r_mcangle_it2.883
r_mcbond_it2.038
r_mcbond_other2.038
r_angle_refined_deg1.764
r_angle_other_deg1.661
r_chiral_restr0.101
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_gen_planes_other0.007
r_bond_other_d0.004
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4049
Nucleic Acid Atoms
Solvent Atoms570
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling