6TN4 | pdb_00006tn4

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
2.8356.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.693α = 90
b = 89.422β = 90
c = 99.829γ = 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
11.27436.31895.90.042117.66.360158
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)
11.2741.38768.30.7480.7391.65.4

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-VALUE1.27436.31857101306777.6350.1730.1720.180.1980.220.296
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]
0.018-0.016-0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.186
r_dihedral_angle_4_deg17.467
r_dihedral_angle_3_deg11.555
r_lrange_it6.729
r_dihedral_angle_1_deg6.468
r_lrange_other6.408
r_scangle_it4.775
r_scangle_other4.773
r_scbond_it3.304
r_scbond_other3.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.186
r_dihedral_angle_4_deg17.467
r_dihedral_angle_3_deg11.555
r_lrange_it6.729
r_dihedral_angle_1_deg6.468
r_lrange_other6.408
r_scangle_it4.775
r_scangle_other4.773
r_scbond_it3.304
r_scbond_other3.302
r_mcangle_it3.158
r_mcangle_other3.157
r_angle_other_deg2.408
r_mcbond_it2.11
r_mcbond_other2.078
r_angle_refined_deg1.957
r_symmetry_xyhbond_nbd_refined0.339
r_symmetry_xyhbond_nbd_other0.292
r_nbd_refined0.23
r_xyhbond_nbd_refined0.213
r_symmetry_nbd_other0.211
r_nbd_other0.179
r_nbtor_refined0.173
r_chiral_restr0.107
r_symmetry_nbtor_other0.074
r_symmetry_nbd_refined0.06
r_bond_other_d0.035
r_bond_refined_d0.016
r_gen_planes_other0.012
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1643
Nucleic Acid Atoms
Solvent Atoms370
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing