X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JZJ4JZJ, 1JLI
experimental modelPDB 1JLI4JZJ, 1JLI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29820% PEG 8000, 200 mM NaCI, 100 mM citrate-phosphate buffer pH 5
Crystal Properties
Matthews coefficientSolvent content
2.8156.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.039α = 90
b = 132.039β = 90
c = 210.631γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.954Australian SynchrotronMX2

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
12.7114.351000.1725.78.130501
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)
12.72.831000.748.5

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 REPLACEMENTTHROUGHOUT4JZJ, 1JLI2.7114.3528930153599.950.244040.241770.28564RANDOM44.007
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]
-1.64-0.82-1.645.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.74
r_dihedral_angle_4_deg16.766
r_dihedral_angle_3_deg15.387
r_dihedral_angle_1_deg6.316
r_long_range_B_refined4.676
r_long_range_B_other4.676
r_mcangle_it2.763
r_mcangle_other2.762
r_scangle_other2.56
r_mcbond_it1.549
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.74
r_dihedral_angle_4_deg16.766
r_dihedral_angle_3_deg15.387
r_dihedral_angle_1_deg6.316
r_long_range_B_refined4.676
r_long_range_B_other4.676
r_mcangle_it2.763
r_mcangle_other2.762
r_scangle_other2.56
r_mcbond_it1.549
r_mcbond_other1.549
r_scbond_it1.455
r_scbond_other1.455
r_angle_refined_deg1.405
r_angle_other_deg1.198
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.004
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 Atoms5964
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms197

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing