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
4.0569.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.347α = 90
b = 102.347β = 90
c = 85.438γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252015-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
11.44102.351000.06219.7882068

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 REPLACEMENTTHROUGHOUT3PAE1.4472.3777950403799.930.113110.112110.13217RANDOM20.713
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]
-0.47-0.470.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.63
r_sphericity_free30.955
r_dihedral_angle_4_deg20.507
r_dihedral_angle_3_deg13.236
r_sphericity_bonded12.688
r_dihedral_angle_1_deg9.047
r_rigid_bond_restr6.611
r_long_range_B_refined4.647
r_long_range_B_other4.646
r_scangle_other4.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.63
r_sphericity_free30.955
r_dihedral_angle_4_deg20.507
r_dihedral_angle_3_deg13.236
r_sphericity_bonded12.688
r_dihedral_angle_1_deg9.047
r_rigid_bond_restr6.611
r_long_range_B_refined4.647
r_long_range_B_other4.646
r_scangle_other4.301
r_scbond_other3.762
r_scbond_it3.761
r_mcangle_it3.496
r_mcangle_other3.495
r_mcbond_it3.301
r_mcbond_other3.3
r_angle_refined_deg2.28
r_angle_other_deg1.031
r_chiral_restr0.214
r_bond_refined_d0.025
r_gen_planes_refined0.013
r_gen_planes_other0.004
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1924
Nucleic Acid Atoms
Solvent Atoms342
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing