6TN5 | pdb_00006tn5

Rapid optimisation of fragments and hits to lead compounds from screening of crude reaction mixtures


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527710% PEG3350, 0.1 M sodium cacodylate pH 6.5, 0.2 M MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.8456.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.72α = 90
b = 89.53β = 90
c = 100.025γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.16554.92591.10.0570.999146.178794
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.1651.24760.90.6540.6861.63.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMIRFREE R-VALUE1.16554.92574921390077.3350.1690.16870.180.18360.1916.209
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]
-0.0020.012-0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.905
r_dihedral_angle_4_deg20.293
r_dihedral_angle_3_deg11.44
r_dihedral_angle_1_deg6.182
r_lrange_it6.069
r_lrange_other5.69
r_scangle_it3.94
r_scangle_other3.938
r_scbond_other2.774
r_scbond_it2.773
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.905
r_dihedral_angle_4_deg20.293
r_dihedral_angle_3_deg11.44
r_dihedral_angle_1_deg6.182
r_lrange_it6.069
r_lrange_other5.69
r_scangle_it3.94
r_scangle_other3.938
r_scbond_other2.774
r_scbond_it2.773
r_mcangle_other2.599
r_mcangle_it2.593
r_angle_other_deg2.387
r_angle_refined_deg2.159
r_mcbond_it1.702
r_mcbond_other1.688
r_symmetry_xyhbond_nbd_other0.464
r_symmetry_xyhbond_nbd_refined0.294
r_xyhbond_nbd_refined0.251
r_nbd_refined0.248
r_symmetry_nbd_other0.216
r_nbd_other0.204
r_nbtor_refined0.178
r_chiral_restr0.111
r_symmetry_nbtor_other0.078
r_symmetry_nbd_refined0.07
r_bond_other_d0.035
r_bond_refined_d0.018
r_gen_planes_other0.016
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1633
Nucleic Acid Atoms
Solvent Atoms395
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing