X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EFJPDB ENTRY 2EFJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529325% PEG 3350, 200mM Li2SO4, 100mM Tris-HCl, 1mM SAH, 1mM xanthosine, 2mM DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3447.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.59α = 90
b = 119.8β = 102.16
c = 116.4γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9393ESRFID14-4

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
12.23095.20.07913.17562474901
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)
12.22.393.40.443310071

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2EFJ2.23071794383096.680.2330.230.284RANDOM44.845
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]
-0.830.42-1.882.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.845
r_dihedral_angle_3_deg19.096
r_dihedral_angle_4_deg12.874
r_dihedral_angle_1_deg6.826
r_scangle_it3.162
r_scbond_it2.093
r_angle_refined_deg1.734
r_mcangle_it1.519
r_mcbond_it0.897
r_symmetry_vdw_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.845
r_dihedral_angle_3_deg19.096
r_dihedral_angle_4_deg12.874
r_dihedral_angle_1_deg6.826
r_scangle_it3.162
r_scbond_it2.093
r_angle_refined_deg1.734
r_mcangle_it1.519
r_mcbond_it0.897
r_symmetry_vdw_refined0.316
r_nbtor_refined0.313
r_symmetry_hbond_refined0.286
r_nbd_refined0.233
r_xyhbond_nbd_refined0.197
r_chiral_restr0.114
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10668
Nucleic Acid Atoms
Solvent Atoms499
Heterogen Atoms184

Software

Software
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing