4KPD

Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CP6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.2M NH4Cl, 20% PEG 6000, 10% Ethelene Glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4249.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.73α = 90
b = 111.73β = 90
c = 66.99γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9796DiamondI02

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
11.9655.8799.40.090.0911.49.630792307922234.9
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)
11.962.07980.85929.42751

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUT3CP61.9655.87223079230728154199.40.1950.19350.2261RANDOM56.93
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]
3.60033.6003-7.2005
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion2.96
t_omega_torsion2.67
t_angle_deg0.95
t_bond_d0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_chiral_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion2.96
t_omega_torsion2.67
t_angle_deg0.95
t_bond_d0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_chiral_improper_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2719
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms34

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling