8JYD

A genetically encoded sensor based on a bacterial DNA ligase


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M MES pH 6.0; 20% PEG mono 2000
Crystal Properties
Matthews coefficientSolvent content
2.5752.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.48α = 90
b = 92.48β = 90
c = 74.29γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDADSC QUANTUM 12023-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.987SSRFBL17U

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
1330.2999.90.130.1360.0310.99925.319.27642
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.081.6320.3690.927

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT330.29724538499.840.217060.21490.2561RANDOM83.024
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]
2.841.422.84-9.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.618
r_dihedral_angle_2_deg9.548
r_dihedral_angle_1_deg6.996
r_long_range_B_refined4.149
r_long_range_B_other4.149
r_mcangle_it3.363
r_mcangle_other3.362
r_scangle_other3.137
r_mcbond_it2.279
r_mcbond_other2.274
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.618
r_dihedral_angle_2_deg9.548
r_dihedral_angle_1_deg6.996
r_long_range_B_refined4.149
r_long_range_B_other4.149
r_mcangle_it3.363
r_mcangle_other3.362
r_scangle_other3.137
r_mcbond_it2.279
r_mcbond_other2.274
r_scbond_it2.13
r_scbond_other2.129
r_angle_refined_deg1.184
r_angle_other_deg0.521
r_chiral_restr0.047
r_bond_other_d0.023
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_gen_planes_other0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2529
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MoRDaphasing