X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6JUL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6297PEG 2KMME 12%, 0.2mM NaCl, Bis Tris Propane 6.0
Crystal Properties
Matthews coefficientSolvent content
2.5551.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.1α = 90
b = 81.03β = 90
c = 210.53γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2016-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.9786ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.1670.1771000.1050.0390.99612.48.450583
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.162.281000.5490.1990.8844.2

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 REPLACEMENTTHROUGHOUT6JUL2.1670.17747928256099.910.203010.200250.25513RANDOM42.932
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]
-1.490.860.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.588
r_dihedral_angle_4_deg18.142
r_dihedral_angle_3_deg16.334
r_long_range_B_refined7.344
r_long_range_B_other7.292
r_dihedral_angle_1_deg6.455
r_scangle_other5.06
r_mcangle_it3.47
r_mcangle_other3.47
r_scbond_it3.324
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.588
r_dihedral_angle_4_deg18.142
r_dihedral_angle_3_deg16.334
r_long_range_B_refined7.344
r_long_range_B_other7.292
r_dihedral_angle_1_deg6.455
r_scangle_other5.06
r_mcangle_it3.47
r_mcangle_other3.47
r_scbond_it3.324
r_scbond_other3.324
r_mcbond_it2.285
r_mcbond_other2.278
r_angle_refined_deg2.187
r_angle_other_deg1.246
r_chiral_restr0.13
r_bond_refined_d0.024
r_gen_planes_refined0.012
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms5298
Nucleic Acid Atoms902
Solvent Atoms422
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building
PHASERphasing