X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.4293.15100 mM Tris(OHAc), 1.3 M (NH4)2SO4
Crystal Properties
Matthews coefficientSolvent content
1.99277738.31544

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.414α = 100.723
b = 50.069β = 102.703
c = 65.584γ = 99.299
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0000SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.548.0896.40.0560.0790.0560.99512.73.381699
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)
11.51.530.180.2550.180.9573.3

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-VALUE1.543.20281698413396.3740.1050.10290.14237.793
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]
0.51-0.289-0.317-0.9140.2050.485
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.187
r_dihedral_angle_2_deg14.173
r_dihedral_angle_3_deg13.788
r_lrange_it10.474
r_lrange_other10.035
r_dihedral_angle_1_deg6.869
r_scangle_it5.221
r_scangle_other5.22
r_scbond_it3.664
r_scbond_other3.664
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.187
r_dihedral_angle_2_deg14.173
r_dihedral_angle_3_deg13.788
r_lrange_it10.474
r_lrange_other10.035
r_dihedral_angle_1_deg6.869
r_scangle_it5.221
r_scangle_other5.22
r_scbond_it3.664
r_scbond_other3.664
r_rigid_bond_restr3.532
r_mcangle_other3.357
r_mcangle_it3.354
r_mcbond_it2.242
r_mcbond_other2.226
r_angle_refined_deg1.667
r_angle_other_deg0.595
r_symmetry_nbd_refined0.269
r_nbd_refined0.236
r_xyhbond_nbd_refined0.215
r_nbd_other0.202
r_symmetry_nbd_other0.193
r_nbtor_refined0.192
r_symmetry_xyhbond_nbd_refined0.191
r_symmetry_xyhbond_nbd_other0.188
r_chiral_restr0.089
r_symmetry_nbtor_other0.081
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4554
Nucleic Acid Atoms
Solvent Atoms507
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction