X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293.15Ammonium Sulfate, Cadmium Sulfate
Crystal Properties
Matthews coefficientSolvent content
3.1961.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 182.594α = 90
b = 182.594β = 90
c = 182.594γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XU1.00SPring-8BL45XU

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
11.8545.691000.070.0990.070.8569.11.822847
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)
11.851.890.0750.1060.0750.9781.9

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-VALUE1dat1.8545.6922823111699.8860.1680.16620.19813.278
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.944
r_dihedral_angle_4_deg22.88
r_dihedral_angle_3_deg13.518
r_lrange_it5.765
r_dihedral_angle_1_deg5.272
r_scangle_it4.351
r_scbond_it2.788
r_mcangle_it1.815
r_angle_refined_deg1.788
r_mcbond_it1.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.944
r_dihedral_angle_4_deg22.88
r_dihedral_angle_3_deg13.518
r_lrange_it5.765
r_dihedral_angle_1_deg5.272
r_scangle_it4.351
r_scbond_it2.788
r_mcangle_it1.815
r_angle_refined_deg1.788
r_mcbond_it1.295
r_symmetry_metal_ion_refined0.342
r_nbtor_refined0.306
r_symmetry_nbd_refined0.274
r_metal_ion_refined0.253
r_nbd_refined0.222
r_xyhbond_nbd_refined0.201
r_symmetry_xyhbond_nbd_refined0.115
r_chiral_restr0.107
r_bond_refined_d0.013
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1363
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building