X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JKB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829320% PEG3350, 0.25M Ammonium sulfate, 0.1M pH8, 7.5% Ethanol
Crystal Properties
Matthews coefficientSolvent content
2.5551.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.134α = 90
b = 73.736β = 90
c = 136.131γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9253DiamondI04

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
11.969136.198.60.09913.93.1107569
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)
11.971.9999.50.5331.933

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 REPLACEMENTTHROUGHOUT2JKB1.97101.05100672528698.520.182950.181250.21519RANDOM31.29
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]
1.74-1.56-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.183
r_dihedral_angle_4_deg13.869
r_dihedral_angle_3_deg13.258
r_dihedral_angle_1_deg7.384
r_long_range_B_refined6.543
r_long_range_B_other6.483
r_scangle_other4.4
r_scbond_it3.066
r_scbond_other2.925
r_mcangle_it2.557
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.183
r_dihedral_angle_4_deg13.869
r_dihedral_angle_3_deg13.258
r_dihedral_angle_1_deg7.384
r_long_range_B_refined6.543
r_long_range_B_other6.483
r_scangle_other4.4
r_scbond_it3.066
r_scbond_other2.925
r_mcangle_it2.557
r_mcangle_other2.557
r_mcbond_it1.831
r_mcbond_other1.831
r_angle_refined_deg1.643
r_angle_other_deg1.091
r_chiral_restr0.1
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.004
r_gen_planes_other0.003
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10396
Nucleic Acid Atoms
Solvent Atoms818
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction