X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5I4B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2M NaAc, 0.1M Na3citrate pH5.5, 10% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
3.1460.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.223α = 90
b = 133.223β = 90
c = 166.786γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-08-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08B1-11.18064CLSI08B1-1

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
12.7547.441000.16110.29.445056
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.752.850.95

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.7547.4445011224199.9360.1740.17050.236260.416
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]
-1.138-0.569-1.1383.691
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.82
r_dihedral_angle_6_deg13.499
r_lrange_other7.044
r_lrange_it7.043
r_dihedral_angle_1_deg6.874
r_scangle_it4.991
r_scangle_other4.991
r_mcangle_it4.898
r_mcangle_other4.898
r_dihedral_angle_2_deg4.757
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.82
r_dihedral_angle_6_deg13.499
r_lrange_other7.044
r_lrange_it7.043
r_dihedral_angle_1_deg6.874
r_scangle_it4.991
r_scangle_other4.991
r_mcangle_it4.898
r_mcangle_other4.898
r_dihedral_angle_2_deg4.757
r_mcbond_it3.241
r_mcbond_other3.241
r_scbond_it3.233
r_scbond_other3.233
r_angle_refined_deg1.028
r_angle_other_deg0.343
r_nbd_refined0.207
r_symmetry_nbd_other0.183
r_nbd_other0.176
r_nbtor_refined0.169
r_symmetry_xyhbond_nbd_refined0.165
r_xyhbond_nbd_refined0.147
r_symmetry_nbd_refined0.099
r_symmetry_nbtor_other0.077
r_chiral_restr0.045
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9550
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing