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
3.1160.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 180.786α = 90
b = 180.786β = 90
c = 180.786γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HE2021-08-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-X1.540562

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
11.512.9599.70.99924.29.840835
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)
11.51.530.943

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-VALUE1dat1.512.9540832206999.6120.1520.15130.166813.431
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_deg36.321
r_dihedral_angle_4_deg19.341
r_dihedral_angle_3_deg13.341
r_lrange_it5.841
r_dihedral_angle_1_deg5.161
r_scangle_it4.116
r_scbond_it2.894
r_mcangle_it1.976
r_angle_refined_deg1.962
r_mcbond_it1.246
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.321
r_dihedral_angle_4_deg19.341
r_dihedral_angle_3_deg13.341
r_lrange_it5.841
r_dihedral_angle_1_deg5.161
r_scangle_it4.116
r_scbond_it2.894
r_mcangle_it1.976
r_angle_refined_deg1.962
r_mcbond_it1.246
r_nbtor_refined0.316
r_symmetry_nbd_refined0.287
r_nbd_refined0.23
r_xyhbond_nbd_refined0.175
r_symmetry_xyhbond_nbd_refined0.159
r_chiral_restr0.106
r_metal_ion_refined0.081
r_bond_refined_d0.012
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1372
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building