1YQ7

Human farnesyl diphosphate synthase complexed with risedronate


X-RAY DIFFRACTION

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-ray100IMAGE PLATERIGAKU RAXIS HTC2005-01-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E1.5418

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
12.255.598.90.08515.86.12215621912
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.3298.9233033

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1UBV2.252.342165421373115598.70.224170.221520.27381RANDOM19.11
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]
-3.7-3.77.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.994
r_dihedral_angle_4_deg19.521
r_dihedral_angle_3_deg17.242
r_scangle_it6.64
r_dihedral_angle_1_deg6.078
r_scbond_it5.326
r_mcangle_it3.258
r_mcbond_it2.215
r_angle_refined_deg1.574
r_angle_other_deg0.834
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.994
r_dihedral_angle_4_deg19.521
r_dihedral_angle_3_deg17.242
r_scangle_it6.64
r_dihedral_angle_1_deg6.078
r_scbond_it5.326
r_mcangle_it3.258
r_mcbond_it2.215
r_angle_refined_deg1.574
r_angle_other_deg0.834
r_mcbond_other0.528
r_nbd_refined0.237
r_xyhbond_nbd_refined0.211
r_nbtor_refined0.195
r_nbd_other0.176
r_symmetry_vdw_other0.146
r_symmetry_hbond_refined0.131
r_symmetry_vdw_refined0.118
r_nbtor_other0.089
r_chiral_restr0.078
r_metal_ion_refined0.049
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 Atoms2654
Nucleic Acid Atoms
Solvent Atoms52
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
PHASERphasing