6TN0 | pdb_00006tn0

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.82770.1 M Sodium acetate pH 5.8 0.125 M Magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
3.2361.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.051α = 90
b = 109.051β = 90
c = 83.945γ = 120
Symmetry
Space GroupP 64

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
11.90594.44194.30.056120.410.327801
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)
11.9052.131.2410.7131.8

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-VALUE1.90594.44127801133262.5990.1780.17580.180.22130.2246.489
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]
0.0020.0010.002-0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.233
r_dihedral_angle_4_deg19.716
r_dihedral_angle_3_deg16.173
r_lrange_other8.848
r_lrange_it8.815
r_scangle_it6.744
r_scangle_other6.742
r_dihedral_angle_1_deg6.435
r_mcangle_it5.353
r_mcangle_other5.351
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.233
r_dihedral_angle_4_deg19.716
r_dihedral_angle_3_deg16.173
r_lrange_other8.848
r_lrange_it8.815
r_scangle_it6.744
r_scangle_other6.742
r_dihedral_angle_1_deg6.435
r_mcangle_it5.353
r_mcangle_other5.351
r_scbond_it4.644
r_scbond_other4.642
r_mcbond_it3.797
r_mcbond_other3.794
r_angle_other_deg2.377
r_angle_refined_deg1.538
r_symmetry_nbd_refined0.271
r_nbd_other0.219
r_symmetry_nbd_other0.215
r_nbd_refined0.213
r_nbtor_refined0.172
r_xyhbond_nbd_refined0.168
r_symmetry_xyhbond_nbd_refined0.087
r_chiral_restr0.076
r_symmetry_nbtor_other0.071
r_bond_other_d0.035
r_gen_planes_other0.01
r_bond_refined_d0.009
r_symmetry_xyhbond_nbd_other0.009
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2718
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing