3TS7

CRYSTAL STRUCTURE OF FARNESYL DIPHOSPHATE SYNTHASE (TARGET EFI-501951) FROM Methylococcus capsulatus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3P41PDB ENTRY 3P41

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52940.1M TRIS-HCL, 2M AMMONIUM PHOSPHATE MONOBASIC, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties
Matthews coefficientSolvent content
2.5952.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.592α = 90
b = 114.592β = 90
c = 113.19γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2011-08-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9450940.131715.356269-537.836
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)
11.941.9796.60.951.114.1

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3P411.945051174163193.850.22060.219150.26577RANDOM47.28
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]
0.330.33-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.565
r_dihedral_angle_3_deg16.839
r_dihedral_angle_4_deg15.396
r_scangle_it11.027
r_scbond_it7.967
r_mcangle_it5.181
r_dihedral_angle_1_deg4.626
r_mcbond_it3.734
r_angle_refined_deg1.292
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.565
r_dihedral_angle_3_deg16.839
r_dihedral_angle_4_deg15.396
r_scangle_it11.027
r_scbond_it7.967
r_mcangle_it5.181
r_dihedral_angle_1_deg4.626
r_mcbond_it3.734
r_angle_refined_deg1.292
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4462
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms25

Software

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