X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6CNZ 
experimental modelPDB 5HPQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293.151:1 volume ratio of 5 mg/ml protein in 20 mM TRIS-HCl, pH=8, 150 uM NaCl buffer and 0.1M BTP, pH=8.5 0.2M KSCN 20% PEG3350
Crystal Properties
Matthews coefficientSolvent content
3.0159.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.608α = 90
b = 105.344β = 112.484
c = 55.776γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 9M2021-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.9762ESRFID30B

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
12.3546.33697.30.9594.13.12093934.2
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)
12.352.44850.4751.1

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-VALUE2.35546.3362091997997.2340.2180.21480.284238.122
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]
-0.155-0.0582.847-1.969
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.852
r_dihedral_angle_3_deg16.804
r_dihedral_angle_6_deg14.974
r_dihedral_angle_1_deg7.206
r_lrange_it6.884
r_lrange_other6.883
r_scangle_it4.466
r_scangle_other4.465
r_mcangle_it4.416
r_mcangle_other4.416
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.852
r_dihedral_angle_3_deg16.804
r_dihedral_angle_6_deg14.974
r_dihedral_angle_1_deg7.206
r_lrange_it6.884
r_lrange_other6.883
r_scangle_it4.466
r_scangle_other4.465
r_mcangle_it4.416
r_mcangle_other4.416
r_scbond_it3.003
r_scbond_other3.003
r_mcbond_it2.975
r_mcbond_other2.97
r_angle_refined_deg1.451
r_angle_other_deg0.511
r_symmetry_xyhbond_nbd_other0.416
r_symmetry_nbd_refined0.326
r_nbd_other0.273
r_symmetry_xyhbond_nbd_refined0.267
r_nbd_refined0.226
r_symmetry_nbd_other0.19
r_xyhbond_nbd_refined0.174
r_nbtor_refined0.171
r_symmetry_nbtor_other0.078
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3087
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing