X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XA7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.25291Sodium Cacodylate 0.085M pH 5.25 + PEG 8K 21% + Glycerol 15%
Crystal Properties
Matthews coefficientSolvent content
2.3647.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.904α = 90
b = 106.78β = 108.092
c = 56.278γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2022-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.9747.8398.70.0770.0350.99810.65.336626
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.972.02991.5780.7470.5341.15.1

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-VALUE1.9747.82936599181498.3980.1970.1950.236747.161
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]
-0.031-0.1830.0210.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.014
r_dihedral_angle_3_deg14.011
r_dihedral_angle_2_deg7.588
r_dihedral_angle_1_deg6.679
r_lrange_it5.886
r_lrange_other5.882
r_scangle_it3.928
r_scangle_other3.927
r_mcangle_it3.435
r_mcangle_other3.434
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.014
r_dihedral_angle_3_deg14.011
r_dihedral_angle_2_deg7.588
r_dihedral_angle_1_deg6.679
r_lrange_it5.886
r_lrange_other5.882
r_scangle_it3.928
r_scangle_other3.927
r_mcangle_it3.435
r_mcangle_other3.434
r_scbond_it2.48
r_scbond_other2.478
r_mcbond_it2.215
r_mcbond_other2.213
r_angle_refined_deg1.073
r_angle_other_deg0.438
r_nbd_refined0.213
r_symmetry_nbd_refined0.205
r_symmetry_nbd_other0.19
r_nbd_other0.19
r_nbtor_refined0.184
r_symmetry_xyhbond_nbd_refined0.155
r_xyhbond_nbd_refined0.152
r_symmetry_nbtor_other0.074
r_chiral_restr0.054
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4214
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing