X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7B53 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52940.1M citrate pH 5.5 13% PEG4K 19.5% 2-propanol
Crystal Properties
Matthews coefficientSolvent content
2.3146.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.59α = 96.72
b = 58.94β = 91.48
c = 74.38γ = 104.47
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2020-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97622DiamondI03

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
11.6856.6970.99912.13.6105615
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)
11.681.720.384

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 REPLACEMENTFREE R-VALUE7B531.6856.6105607528696.9810.1990.1970.239237.212
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]
-0.6260.7150.0360.2261.149-0.341
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.527
r_dihedral_angle_4_deg16.521
r_dihedral_angle_3_deg12.886
r_lrange_it7.244
r_lrange_other7.228
r_dihedral_angle_1_deg6.702
r_scangle_it6.011
r_scangle_other6.01
r_mcangle_other4.013
r_mcangle_it4.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.527
r_dihedral_angle_4_deg16.521
r_dihedral_angle_3_deg12.886
r_lrange_it7.244
r_lrange_other7.228
r_dihedral_angle_1_deg6.702
r_scangle_it6.011
r_scangle_other6.01
r_mcangle_other4.013
r_mcangle_it4.012
r_scbond_it3.988
r_scbond_other3.988
r_mcbond_it2.931
r_mcbond_other2.928
r_angle_refined_deg1.543
r_angle_other_deg1.375
r_symmetry_xyhbond_nbd_refined0.228
r_nbd_refined0.208
r_symmetry_nbd_other0.172
r_xyhbond_nbd_refined0.166
r_nbtor_refined0.156
r_nbd_other0.153
r_symmetry_nbd_refined0.142
r_symmetry_xyhbond_nbd_other0.141
r_xyhbond_nbd_other0.113
r_symmetry_nbtor_other0.078
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7217
Nucleic Acid Atoms
Solvent Atoms337
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing