X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.8293peg4k 25% , 0.1M MES 5.8 buffer
Crystal Properties
Matthews coefficientSolvent content
2.1342.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.898α = 90
b = 73.032β = 90
c = 240.864γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray170PIXELDECTRIS PILATUS 200K2021-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
12.25074.50.150.3110.7715.43.236438
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)
12.22.2846.10.7711.6

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-VALUE1dic2.21446.4634591169485.1640.2290.2250.299833.495
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]
-0.0480.06-0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.685
r_dihedral_angle_3_deg16.172
r_dihedral_angle_6_deg14.435
r_dihedral_angle_1_deg7.637
r_lrange_it7.311
r_lrange_other7.307
r_mcangle_other4.261
r_mcangle_it4.26
r_scangle_it4.219
r_scangle_other4.219
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.685
r_dihedral_angle_3_deg16.172
r_dihedral_angle_6_deg14.435
r_dihedral_angle_1_deg7.637
r_lrange_it7.311
r_lrange_other7.307
r_mcangle_other4.261
r_mcangle_it4.26
r_scangle_it4.219
r_scangle_other4.219
r_mcbond_it2.762
r_mcbond_other2.762
r_scbond_it2.756
r_scbond_other2.756
r_angle_refined_deg1.372
r_chiral_restr_other1.007
r_angle_other_deg0.533
r_symmetry_xyhbond_nbd_refined0.343
r_symmetry_nbd_refined0.229
r_nbd_other0.229
r_nbd_refined0.217
r_symmetry_nbd_other0.199
r_nbtor_refined0.163
r_xyhbond_nbd_refined0.153
r_symmetry_nbtor_other0.082
r_chiral_restr0.056
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6484
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms120

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing