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
3.0759.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 180.213α = 90
b = 180.213β = 90
c = 180.213γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HE2021-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-X1.540562

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
11.912.9199.70.0910.0960.030.99821.59.520252
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)
11.91.941000.5570.6060.2370.8773.2

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-VALUE1dat1.912.9092025099199.4890.1720.170.208516.605
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_deg33.588
r_dihedral_angle_4_deg21.441
r_dihedral_angle_3_deg14.546
r_lrange_it6.117
r_dihedral_angle_1_deg5.212
r_scangle_it4.454
r_scbond_it2.975
r_mcangle_it2.315
r_angle_refined_deg1.775
r_mcbond_it1.602
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.588
r_dihedral_angle_4_deg21.441
r_dihedral_angle_3_deg14.546
r_lrange_it6.117
r_dihedral_angle_1_deg5.212
r_scangle_it4.454
r_scbond_it2.975
r_mcangle_it2.315
r_angle_refined_deg1.775
r_mcbond_it1.602
r_nbtor_refined0.311
r_symmetry_nbd_refined0.232
r_nbd_refined0.227
r_xyhbond_nbd_refined0.2
r_symmetry_xyhbond_nbd_refined0.179
r_chiral_restr0.106
r_metal_ion_refined0.095
r_symmetry_metal_ion_refined0.095
r_bond_refined_d0.012
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1363
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building