X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4D0N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52932.6 M sodium formate, 100 mM Tris
Crystal Properties
Matthews coefficientSolvent content
2.5351.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.432α = 90
b = 71.432β = 90
c = 196.527γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2022-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9212DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.471.431000.0720.99910.345.8101036
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4299.93.1320.4030.722.9

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-VALUE4D0N1.457.845100884200099.9720.1310.12970.175119.506
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]
0.3070.307-0.614
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.665
r_dihedral_angle_3_deg13.245
r_dihedral_angle_2_deg8.248
r_scangle_it6.091
r_scangle_other6.091
r_scbond_it5.737
r_scbond_other5.602
r_dihedral_angle_1_deg5.566
r_lrange_it5.512
r_lrange_other5.451
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.665
r_dihedral_angle_3_deg13.245
r_dihedral_angle_2_deg8.248
r_scangle_it6.091
r_scangle_other6.091
r_scbond_it5.737
r_scbond_other5.602
r_dihedral_angle_1_deg5.566
r_lrange_it5.512
r_lrange_other5.451
r_rigid_bond_restr5.15
r_mcangle_it3.547
r_mcangle_other3.546
r_mcbond_other2.91
r_mcbond_it2.909
r_angle_refined_deg1.64
r_angle_other_deg0.609
r_nbd_refined0.256
r_xyhbond_nbd_refined0.244
r_symmetry_xyhbond_nbd_refined0.198
r_symmetry_nbd_other0.178
r_nbtor_refined0.172
r_nbd_other0.171
r_symmetry_nbd_refined0.155
r_chiral_restr0.091
r_symmetry_nbtor_other0.074
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3427
Nucleic Acid Atoms
Solvent Atoms451
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing