X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5T2Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.62982.1M Sodium chloride, 0.1M HEPES pH 7.6
Crystal Properties
Matthews coefficientSolvent content
2.550.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.704α = 90
b = 60.358β = 90.93
c = 66.476γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2016-02-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.75099.50.0760.04517.13.946434
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7699.60.4180.4180.2420.8866.13.8

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 REPLACEMENTTHROUGHOUT5T2Z1.734.5344127229199.20.177660.175810.21179RANDOM21.102
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]
-0.38-0.58-0.130.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.299
r_dihedral_angle_3_deg12.091
r_dihedral_angle_4_deg10.947
r_dihedral_angle_1_deg7.099
r_long_range_B_other6.449
r_long_range_B_refined6.447
r_scangle_other5.401
r_scbond_it3.609
r_scbond_other3.608
r_angle_other_deg3.595
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.299
r_dihedral_angle_3_deg12.091
r_dihedral_angle_4_deg10.947
r_dihedral_angle_1_deg7.099
r_long_range_B_other6.449
r_long_range_B_refined6.447
r_scangle_other5.401
r_scbond_it3.609
r_scbond_other3.608
r_angle_other_deg3.595
r_mcangle_it3.018
r_mcangle_other3.017
r_angle_refined_deg2.218
r_mcbond_it2.133
r_mcbond_other2.132
r_chiral_restr0.141
r_bond_refined_d0.024
r_gen_planes_other0.02
r_gen_planes_refined0.013
r_bond_other_d
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 Atoms3044
Nucleic Acid Atoms
Solvent Atoms170
Heterogen Atoms131

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing