X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q8F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP291.1590 mM PIPES pH 7.0, 90 mM MgCl2, 45 mM KCl, 1 mM NiSO4, 14% (w/v) PEG 5000 monomethyl ether
Crystal Properties
Matthews coefficientSolvent content
2.5251.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.344α = 90
b = 92.344β = 90
c = 185.111γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MToroidal mirror2020-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9724ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
11.8546.32198.80.1490.0270.99915.121.568295
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.8989.11.4780.5190.6251.28.2

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 REPLACEMENTTHROUGHOUT1.8546.32168100345598.5830.1850.18370.201141.685
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]
-1.47-1.472.939
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.026
r_dihedral_angle_3_deg13.557
r_dihedral_angle_1_deg6.46
r_lrange_it6.224
r_lrange_other6.173
r_dihedral_angle_2_deg4.99
r_scangle_it3.721
r_scangle_other3.72
r_mcangle_other2.556
r_mcangle_it2.555
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.026
r_dihedral_angle_3_deg13.557
r_dihedral_angle_1_deg6.46
r_lrange_it6.224
r_lrange_other6.173
r_dihedral_angle_2_deg4.99
r_scangle_it3.721
r_scangle_other3.72
r_mcangle_other2.556
r_mcangle_it2.555
r_scbond_it2.261
r_scbond_other2.261
r_mcbond_it1.736
r_mcbond_other1.64
r_angle_refined_deg1.038
r_angle_other_deg0.358
r_nbd_refined0.204
r_symmetry_nbd_other0.181
r_nbtor_refined0.177
r_symmetry_xyhbond_nbd_refined0.171
r_xyhbond_nbd_refined0.154
r_nbd_other0.145
r_symmetry_nbd_refined0.133
r_ncsr_local_group_10.098
r_symmetry_nbtor_other0.075
r_symmetry_xyhbond_nbd_other0.056
r_chiral_restr0.054
r_bond_refined_d0.004
r_dihedral_angle_other_3_deg0.004
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 Atoms5468
Nucleic Acid Atoms
Solvent Atoms358
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing