X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3D4XPDB ENTRY 3D4X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.729340% PEG 3350, 50mM phosphate buffer at pH 6.7, 1M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4349.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.022α = 90
b = 96.465β = 90
c = 146.345γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMAR scanner 345 mm plate2007-10-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5417

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.930960.0984.13.65268002388622
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.9398.50.26481.43.142304

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 3D4X2.924.13222680023762265695.990.195620.187120.27106RANDOM48.397
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]
-1.751.160.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.766
r_dihedral_angle_3_deg21.027
r_dihedral_angle_4_deg12.081
r_dihedral_angle_1_deg5.972
r_angle_refined_deg1.583
r_mcbond_it0.818
r_nbtor_refined0.308
r_symmetry_hbond_refined0.291
r_symmetry_vdw_refined0.271
r_nbd_refined0.248
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.766
r_dihedral_angle_3_deg21.027
r_dihedral_angle_4_deg12.081
r_dihedral_angle_1_deg5.972
r_angle_refined_deg1.583
r_mcbond_it0.818
r_nbtor_refined0.308
r_symmetry_hbond_refined0.291
r_symmetry_vdw_refined0.271
r_nbd_refined0.248
r_xyhbond_nbd_refined0.151
r_chiral_restr0.102
r_metal_ion_refined0.022
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_mcangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8685
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms344

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
AUTOMARdata reduction
SCALEPACKdata scaling