1YV5

Human farnesyl diphosphate synthase complexed with Mg and risedronate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UBV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.229340% PEG 300, 0.1M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.453

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.946α = 90
b = 110.946β = 90
c = 70.264γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.16ALS8.3.1

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
1270.299.90.0920.0928.7302423021234.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.111002.28.64319

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1UBV252.342865628467152999.340.207650.207650.205490.24888RANDOM25.087
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]
-3.2-3.26.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.077
r_dihedral_angle_4_deg18.511
r_dihedral_angle_3_deg14.515
r_scangle_it6.838
r_dihedral_angle_1_deg5.484
r_scbond_it5.361
r_mcangle_it3.248
r_mcbond_it2.122
r_angle_refined_deg1.531
r_angle_other_deg0.824
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.077
r_dihedral_angle_4_deg18.511
r_dihedral_angle_3_deg14.515
r_scangle_it6.838
r_dihedral_angle_1_deg5.484
r_scbond_it5.361
r_mcangle_it3.248
r_mcbond_it2.122
r_angle_refined_deg1.531
r_angle_other_deg0.824
r_mcbond_other0.54
r_nbd_refined0.218
r_nbtor_refined0.195
r_nbd_other0.17
r_symmetry_vdw_refined0.163
r_xyhbond_nbd_refined0.159
r_symmetry_vdw_other0.151
r_metal_ion_refined0.142
r_symmetry_hbond_refined0.132
r_nbtor_other0.087
r_chiral_restr0.082
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_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 Atoms2650
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
PHASERphasing