1ZW5

X-ray structure of Farnesyl diphosphate synthase protein


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP429314% PEG 6000, 0.7 M LiCl, 70 mM citrate pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4449.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.255α = 90
b = 112.255β = 90
c = 63.245γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.984SLSX10SA

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
12.36395.60.10.1113.95.2183231751738
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.4297.92.75.2

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1YV52.330175531660588694.590.175080.175080.172490.22311RANDOM46.785
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]
-3.86-3.867.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.947
r_dihedral_angle_4_deg16.52
r_dihedral_angle_3_deg15.64
r_scangle_it7.394
r_scbond_it5.873
r_dihedral_angle_1_deg5.53
r_mcangle_it3.529
r_mcbond_it2.427
r_angle_refined_deg1.504
r_angle_other_deg0.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.947
r_dihedral_angle_4_deg16.52
r_dihedral_angle_3_deg15.64
r_scangle_it7.394
r_scbond_it5.873
r_dihedral_angle_1_deg5.53
r_mcangle_it3.529
r_mcbond_it2.427
r_angle_refined_deg1.504
r_angle_other_deg0.84
r_mcbond_other0.648
r_symmetry_vdw_other0.239
r_nbd_refined0.211
r_symmetry_hbond_refined0.203
r_nbtor_refined0.185
r_nbd_other0.172
r_xyhbond_nbd_refined0.139
r_symmetry_vdw_refined0.13
r_nbtor_other0.087
r_chiral_restr0.079
r_metal_ion_refined0.047
r_bond_refined_d0.015
r_gen_planes_refined0.005
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 Atoms2697
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling