X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527732% PEG 3350, 0.2 M ammonium sulfate, 20 mM sodium cacodylate, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.244.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.795α = 90
b = 66.352β = 90
c = 68.287γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2017-10-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.00000APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Rpim I (All)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
11.737.2399.970.1560.0650.72213.815.129059212.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.737.2399.860.6450.7190.3090.74825

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 REPLACEMENTTHROUGHOUT3IXF1.737.2329059148299.970.165390.162230.22732RANDOM15.617
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]
2.48-15.6313.14
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.518
r_dihedral_angle_2_deg36.009
r_dihedral_angle_4_deg21.082
r_dihedral_angle_3_deg15.764
r_sphericity_bonded11.122
r_dihedral_angle_1_deg5.513
r_long_range_B_refined4.011
r_long_range_B_other4.011
r_scangle_other2.978
r_scbond_it2.559
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.518
r_dihedral_angle_2_deg36.009
r_dihedral_angle_4_deg21.082
r_dihedral_angle_3_deg15.764
r_sphericity_bonded11.122
r_dihedral_angle_1_deg5.513
r_long_range_B_refined4.011
r_long_range_B_other4.011
r_scangle_other2.978
r_scbond_it2.559
r_scbond_other2.559
r_rigid_bond_restr2.497
r_mcangle_it2.2
r_mcangle_other2.199
r_angle_refined_deg1.712
r_mcbond_other1.637
r_mcbond_it1.636
r_angle_other_deg1.086
r_chiral_restr0.125
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_gen_planes_other0.005
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 Atoms2154
Nucleic Acid Atoms
Solvent Atoms289
Heterogen Atoms124

Software

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