X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277MPEG 2000, ammonium sulfate, Na cacodylate
Crystal Properties
Matthews coefficientSolvent content
2.1643.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.657α = 90
b = 66.492β = 90
c = 68.34γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.6634.19397.30.97515.33.731407
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.661.7030.447

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3IXF1.6634.19331407160297.3140.1690.16590.234124.037
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]
-1.979-1.2953.274
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.897
r_dihedral_angle_4_deg19.866
r_dihedral_angle_3_deg17.554
r_rigid_bond_restr11.791
r_scangle_it7.093
r_lrange_it7.077
r_lrange_other7.031
r_scangle_other6.741
r_scbond_it5.788
r_scbond_other5.592
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.897
r_dihedral_angle_4_deg19.866
r_dihedral_angle_3_deg17.554
r_rigid_bond_restr11.791
r_scangle_it7.093
r_lrange_it7.077
r_lrange_other7.031
r_scangle_other6.741
r_scbond_it5.788
r_scbond_other5.592
r_dihedral_angle_1_deg5.364
r_mcangle_other4.213
r_mcangle_it4.207
r_mcbond_it3.499
r_mcbond_other3.431
r_angle_refined_deg1.83
r_angle_other_deg1.568
r_symmetry_nbd_refined0.298
r_nbd_other0.275
r_nbd_refined0.27
r_symmetry_nbd_other0.229
r_nbtor_refined0.187
r_xyhbond_nbd_refined0.169
r_symmetry_xyhbond_nbd_refined0.136
r_chiral_restr0.094
r_symmetry_nbtor_other0.082
r_symmetry_xyhbond_nbd_other0.061
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_gen_planes_other0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2132
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms164

Software

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