2OPM

Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-461


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.229810% PEG 2K, 0.5M Phosphate Citrate buffer, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3349.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.783α = 90
b = 111.783β = 90
c = 66.525γ = 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
12.45098.60.110.412.216818
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)
12.42.49920.4129.2

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 1YV52.430159181591883893.70.23350.23350.2693RANDOM
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
2868.5
RMS Deviations
KeyRefinement Restraint Deviation
s_similar_adp_cmpnt0.086
s_non_zero_chiral_vol0.023
s_zero_chiral_vol0.018
s_from_restr_planes0.0175
s_angle_d0.016
s_anti_bump_dis_restr0.007
s_bond_d0.004
s_similar_dist
s_rigid_bond_adp_cmpnt
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2707
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms31

Software

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