8AHG | pdb_00008ahg

PAC-FragmentDEL: Photoactivated covalent capture of DNA encoded fragments for hit discovery


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BVA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52770.8M Na/K tartrate 0.1M Tris pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.4348.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.822α = 90
b = 61.822β = 90
c = 180.79γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.88558.49695.30.090.0920.018122.726.427812
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)
11.8851.95250.63.0583.1150.5880.638127.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2BVA1.88558.49627811138794.9080.1810.17850.190.22650.2338.439
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]
-0.051-0.0510.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.742
r_dihedral_angle_6_deg16.412
r_lrange_it7.424
r_lrange_other7.387
r_dihedral_angle_1_deg7.183
r_dihedral_angle_2_deg6.122
r_scangle_it5.92
r_scangle_other5.919
r_scbond_it4.244
r_scbond_other4.242
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.742
r_dihedral_angle_6_deg16.412
r_lrange_it7.424
r_lrange_other7.387
r_dihedral_angle_1_deg7.183
r_dihedral_angle_2_deg6.122
r_scangle_it5.92
r_scangle_other5.919
r_scbond_it4.244
r_scbond_other4.242
r_mcangle_it4.159
r_mcangle_other4.159
r_mcbond_it3.397
r_mcbond_other3.394
r_angle_refined_deg1.539
r_angle_other_deg0.524
r_symmetry_xyhbond_nbd_refined0.279
r_nbd_refined0.213
r_nbd_other0.21
r_xyhbond_nbd_refined0.204
r_symmetry_nbd_refined0.204
r_symmetry_nbd_other0.192
r_nbtor_refined0.17
r_symmetry_nbtor_other0.08
r_chiral_restr0.078
r_symmetry_xyhbond_nbd_other0.048
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2308
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building