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
4.1570.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.974α = 90
b = 102.974β = 90
c = 86.73γ = 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
11.75102.97950.087127.345159

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 REPLACEMENTTHROUGHOUT3PAE1.7572.8142819230894.920.17920.177770.20735RANDOM32.97
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]
-1.94-1.943.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.904
r_dihedral_angle_4_deg19.002
r_dihedral_angle_3_deg12.496
r_long_range_B_refined8.146
r_dihedral_angle_1_deg8.118
r_long_range_B_other8.065
r_scangle_other6.692
r_scbond_it4.275
r_scbond_other4.273
r_mcangle_other4.108
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.904
r_dihedral_angle_4_deg19.002
r_dihedral_angle_3_deg12.496
r_long_range_B_refined8.146
r_dihedral_angle_1_deg8.118
r_long_range_B_other8.065
r_scangle_other6.692
r_scbond_it4.275
r_scbond_other4.273
r_mcangle_other4.108
r_mcangle_it4.1
r_mcbond_it2.822
r_mcbond_other2.788
r_angle_refined_deg1.849
r_angle_other_deg0.965
r_chiral_restr0.154
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms1925
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing