2OPN

Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-527


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YV5pdb entry 1YV5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.210% PEG 4K, 0.5M Phosphate Citrate buffer, pH 4.2, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.3349.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.652α = 90
b = 111.652β = 90
c = 66.841γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray123.2CCDADSC QUANTUM 3152005-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
12.450990.1078.311.312031
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)
12.42.4997.70.3838.4

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 REPLACEMENTFREE Rpdb entry 1YV52.7301137011370600940.27240.27240.2979RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
12777.62
RMS Deviations
KeyRefinement Restraint Deviation
s_similar_adp_cmpnt0.084
s_anti_bump_dis_restr0.03
s_zero_chiral_vol0.027
s_non_zero_chiral_vol0.027
s_from_restr_planes0.0155
s_angle_d0.014
s_bond_d0.006
s_similar_dist
s_rigid_bond_adp_cmpnt
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2659
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms27

Software

Software
Software NamePurpose
AMoREphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling