3B7L

Human farnesyl diphosphate synthase complexed with MG and minodronate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YV5PDB entry 1YV5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.2M NH4Cl, 20% PEG 6000, 10% Ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5351.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.922α = 90
b = 110.922β = 90
c = 67.308γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTCOSMIC mirrors2007-08-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.9520.4499.20.0650.02720.66.831186309372
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0695.30.6060.272.35.74240

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 1YV51.9520.213093729320157399.250.170780.169070.2022RANDOM28.864
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]
-0.92-0.921.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.415
r_dihedral_angle_4_deg17.959
r_dihedral_angle_3_deg13.61
r_scangle_it7.711
r_scbond_it6.085
r_dihedral_angle_1_deg5.726
r_mcangle_it3.637
r_mcbond_it2.74
r_angle_refined_deg1.47
r_angle_other_deg1.353
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.415
r_dihedral_angle_4_deg17.959
r_dihedral_angle_3_deg13.61
r_scangle_it7.711
r_scbond_it6.085
r_dihedral_angle_1_deg5.726
r_mcangle_it3.637
r_mcbond_it2.74
r_angle_refined_deg1.47
r_angle_other_deg1.353
r_mcbond_other0.827
r_nbd_refined0.208
r_symmetry_vdw_other0.196
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.18
r_nbd_other0.179
r_symmetry_hbond_refined0.131
r_nbtor_other0.088
r_chiral_restr0.085
r_symmetry_vdw_refined0.045
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2718
Nucleic Acid Atoms
Solvent Atoms268
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing