X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7CAQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.075 M succinic acid, pH7.0, 11% PEG 3350, and 25% glycerol, 3 mM farnesyl pyrophosphate (FPP), 0.3 mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.3146.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.853α = 90
b = 98.91β = 90
c = 193.853γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2018-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.000Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.9148.461000.68833.622.3147512
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.911.942.050.688

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7CAQ1.9147.92147470754199.8140.1970.19630.219542.591
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]
0.0050.007-0.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.609
r_dihedral_angle_4_deg20.898
r_dihedral_angle_3_deg15.048
r_dihedral_angle_1_deg6.388
r_lrange_it6.197
r_lrange_other6.185
r_scangle_it4.317
r_scangle_other4.3
r_mcangle_it3.559
r_mcangle_other3.559
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.609
r_dihedral_angle_4_deg20.898
r_dihedral_angle_3_deg15.048
r_dihedral_angle_1_deg6.388
r_lrange_it6.197
r_lrange_other6.185
r_scangle_it4.317
r_scangle_other4.3
r_mcangle_it3.559
r_mcangle_other3.559
r_scbond_it2.877
r_scbond_other2.844
r_mcbond_it2.581
r_mcbond_other2.581
r_angle_other_deg2.263
r_angle_refined_deg1.306
r_symmetry_nbd_other0.219
r_nbd_other0.201
r_nbd_refined0.197
r_symmetry_xyhbond_nbd_refined0.172
r_nbtor_refined0.163
r_xyhbond_nbd_refined0.158
r_symmetry_nbd_refined0.125
r_symmetry_xyhbond_nbd_other0.071
r_chiral_restr0.063
r_symmetry_nbtor_other0.062
r_metal_ion_refined0.055
r_bond_other_d0.034
r_gen_planes_other0.007
r_bond_refined_d0.005
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13896
Nucleic Acid Atoms
Solvent Atoms485
Heterogen Atoms272

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing