X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PAE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5298100 mM TRIS-HCl, pH 8.5, 2.0 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
4.1770.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.418α = 90
b = 102.418β = 90
c = 85.049γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2016-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.12713APS21-ID-D

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
11.7886.6893.70.09412.47.341363

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 REPLACEMENTTHROUGHOUT3PAE1.7872.4239199210493.550.168740.167450.19244RANDOM27.738
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]
-1.13-1.132.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.411
r_dihedral_angle_4_deg16.647
r_dihedral_angle_3_deg12.988
r_long_range_B_refined6.294
r_long_range_B_other6.139
r_dihedral_angle_1_deg5.476
r_scangle_other5.007
r_scbond_it3.229
r_scbond_other3.208
r_mcangle_other3.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.411
r_dihedral_angle_4_deg16.647
r_dihedral_angle_3_deg12.988
r_long_range_B_refined6.294
r_long_range_B_other6.139
r_dihedral_angle_1_deg5.476
r_scangle_other5.007
r_scbond_it3.229
r_scbond_other3.208
r_mcangle_other3.097
r_mcangle_it3.096
r_mcbond_it2.063
r_mcbond_other2.048
r_angle_refined_deg1.527
r_angle_other_deg0.942
r_chiral_restr0.091
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms1919
Nucleic Acid Atoms
Solvent Atoms199
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing