X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52982% PEG 400, 2M K2HPO4/NaH2PO4, 3mM farnesyl thiopyrophosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5651.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.888α = 90
b = 153.752β = 91.06
c = 91.613γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTCVariMaxHF2010-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54178

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
12.353099.10.079234.69879497910149.7
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)
12.352.4598.70.6553.64.39803

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3VJB2.353097681487698.670.193640.190350.25697RANDOM56.082
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]
-0.4-0.150.49-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.265
r_dihedral_angle_3_deg18.717
r_dihedral_angle_4_deg16.836
r_scangle_it5.78
r_dihedral_angle_1_deg5.213
r_scbond_it3.457
r_mcangle_it2.902
r_rigid_bond_restr1.804
r_mcbond_it1.549
r_angle_refined_deg1.417
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.265
r_dihedral_angle_3_deg18.717
r_dihedral_angle_4_deg16.836
r_scangle_it5.78
r_dihedral_angle_1_deg5.213
r_scbond_it3.457
r_mcangle_it2.902
r_rigid_bond_restr1.804
r_mcbond_it1.549
r_angle_refined_deg1.417
r_chiral_restr0.099
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15961
Nucleic Acid Atoms
Solvent Atoms352
Heterogen Atoms192

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling