X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7BRO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82950.1 M imidazole pH 8, 0.1 M LiSO4, 1 mM DTT, 12% PEG 3000
Crystal Properties
Matthews coefficientSolvent content
2.0138.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.867α = 90
b = 53.4β = 101.111
c = 113.373γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2022-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0ALS5.0.2

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
11.7848.1997.60.0880.0960.0360.99910.96.825214
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)
11.781.8297.22.2592.440.9120.4290.86.9

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-VALUE1.78148.18725178199697.1860.1960.19260.228440.617
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]
-0.940.6620.0370.598
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_other_3_deg16.675
r_dihedral_angle_3_deg15.915
r_dihedral_angle_6_deg13.673
r_dihedral_angle_2_deg10.467
r_dihedral_angle_1_deg7.257
r_dihedral_angle_other_2_deg7.07
r_lrange_it6.454
r_lrange_other6.384
r_scangle_it3.904
r_scangle_other3.903
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_other_3_deg16.675
r_dihedral_angle_3_deg15.915
r_dihedral_angle_6_deg13.673
r_dihedral_angle_2_deg10.467
r_dihedral_angle_1_deg7.257
r_dihedral_angle_other_2_deg7.07
r_lrange_it6.454
r_lrange_other6.384
r_scangle_it3.904
r_scangle_other3.903
r_mcangle_it2.812
r_mcangle_other2.811
r_scbond_it2.454
r_scbond_other2.454
r_mcbond_it1.83
r_mcbond_other1.83
r_angle_other_deg1.599
r_angle_refined_deg1.422
r_symmetry_xyhbond_nbd_other0.421
r_nbd_refined0.247
r_nbd_other0.232
r_symmetry_nbd_other0.223
r_symmetry_nbd_refined0.19
r_xyhbond_nbd_refined0.184
r_nbtor_refined0.183
r_symmetry_xyhbond_nbd_refined0.161
r_symmetry_nbtor_other0.087
r_chiral_restr0.068
r_gen_planes_other0.007
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2361
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing