X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6SDR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29322% PEG 3350 (w/v), 0.1 M Tris-HCl pH 8.5 and 0.2 M CaCl2
Crystal Properties
Matthews coefficientSolvent content
2.346.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.299α = 90
b = 126.897β = 90
c = 260.94γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979181ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.3148.1299.50.998.44.5108727
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.370.698

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-VALUE6sdr2.348.312108727542799.7790.2030.20040.256142.628
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]
-2.3083.506-1.198
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.174
r_dihedral_angle_4_deg18.154
r_dihedral_angle_3_deg15.125
r_dihedral_angle_1_deg7.309
r_lrange_it5.701
r_lrange_other5.698
r_scangle_it4.001
r_scangle_other4.001
r_mcangle_it3.677
r_mcangle_other3.677
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.174
r_dihedral_angle_4_deg18.154
r_dihedral_angle_3_deg15.125
r_dihedral_angle_1_deg7.309
r_lrange_it5.701
r_lrange_other5.698
r_scangle_it4.001
r_scangle_other4.001
r_mcangle_it3.677
r_mcangle_other3.677
r_scbond_it2.446
r_scbond_other2.446
r_mcbond_it2.369
r_mcbond_other2.367
r_angle_refined_deg1.399
r_angle_other_deg1.152
r_nbd_refined0.192
r_nbd_other0.181
r_symmetry_nbd_other0.18
r_nbtor_refined0.162
r_xyhbond_nbd_refined0.151
r_symmetry_nbd_refined0.126
r_symmetry_xyhbond_nbd_refined0.109
r_symmetry_xyhbond_nbd_other0.079
r_symmetry_nbtor_other0.075
r_chiral_restr0.072
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms18540
Nucleic Acid Atoms
Solvent Atoms356
Heterogen Atoms291

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing