X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SXR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1M Imidazole pH6.5, 20% PEG 8000, 3% MPD
Crystal Properties
Matthews coefficientSolvent content
2.3146.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.372α = 90
b = 67.475β = 90
c = 76.519γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2023-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.953714CLSI08ID-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
11.344.999.40.07419.213.170778
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)
11.31.330.979

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-VALUE1.344.89970698349499.3660.1290.12780.160618.648
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]
1.7060.168-1.874
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_other_3_deg48.358
r_dihedral_angle_2_deg31.423
r_dihedral_angle_4_deg19.243
r_dihedral_angle_3_deg10.885
r_dihedral_angle_1_deg6.339
r_lrange_it4.3
r_lrange_other3.87
r_scangle_it2.67
r_scangle_other2.67
r_scbond_it2.326
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_other_3_deg48.358
r_dihedral_angle_2_deg31.423
r_dihedral_angle_4_deg19.243
r_dihedral_angle_3_deg10.885
r_dihedral_angle_1_deg6.339
r_lrange_it4.3
r_lrange_other3.87
r_scangle_it2.67
r_scangle_other2.67
r_scbond_it2.326
r_scbond_other2.325
r_rigid_bond_restr2.319
r_mcangle_it1.826
r_mcangle_other1.826
r_angle_refined_deg1.723
r_angle_other_deg1.51
r_mcbond_other1.344
r_mcbond_it1.343
r_symmetry_nbd_refined0.236
r_nbd_refined0.213
r_nbd_other0.199
r_nbtor_refined0.183
r_symmetry_nbd_other0.182
r_symmetry_xyhbond_nbd_refined0.178
r_xyhbond_nbd_refined0.171
r_chiral_restr0.097
r_symmetry_nbtor_other0.084
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_gen_planes_other0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2119
Nucleic Acid Atoms
Solvent Atoms388
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing