X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4OKMPDB entry 4OKM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82930.1 M TRIS, 200 mM MgCl2, 24% PEG 3350, 1 mM dihydrofarnesyl pyrophosphate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4850.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.09α = 90
b = 117.78β = 90
c = 185.59γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-09-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
11.94099.60.04723.84.513009012957022
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)
11.9299.60.4184.3

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 REPLACEMENTTHROUGHOUTPDB entry 4OKM1.915129570123091647999.570.144460.142720.17711RANDOM28.674
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]
-0.812.74-1.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.657
r_sphericity_free27.894
r_dihedral_angle_4_deg18.853
r_dihedral_angle_3_deg14.373
r_sphericity_bonded7.455
r_dihedral_angle_1_deg4.729
r_rigid_bond_restr1.414
r_angle_refined_deg1.125
r_angle_other_deg0.869
r_chiral_restr0.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.657
r_sphericity_free27.894
r_dihedral_angle_4_deg18.853
r_dihedral_angle_3_deg14.373
r_sphericity_bonded7.455
r_dihedral_angle_1_deg4.729
r_rigid_bond_restr1.414
r_angle_refined_deg1.125
r_angle_other_deg0.869
r_chiral_restr0.069
r_bond_refined_d0.007
r_bond_other_d0.003
r_gen_planes_refined0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11006
Nucleic Acid Atoms
Solvent Atoms1189
Heterogen Atoms108

Software

Software
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling