6TMZ | pdb_00006tmz

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
3.362.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.379α = 90
b = 110.379β = 90
c = 83.679γ = 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
12.6695.59191.80.105117.11010734
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)
12.662.9283.11.3330.6331.710.2

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-VALUE2.7155.1891068755663.7080.1970.19360.20.26190.2665.226
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]
-0.222-0.111-0.2220.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.976
r_dihedral_angle_4_deg23.688
r_dihedral_angle_3_deg19.628
r_lrange_it11.83
r_lrange_other11.829
r_scangle_it8.871
r_scangle_other8.869
r_mcangle_it8.621
r_mcangle_other8.618
r_dihedral_angle_1_deg8.054
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.976
r_dihedral_angle_4_deg23.688
r_dihedral_angle_3_deg19.628
r_lrange_it11.83
r_lrange_other11.829
r_scangle_it8.871
r_scangle_other8.869
r_mcangle_it8.621
r_mcangle_other8.618
r_dihedral_angle_1_deg8.054
r_mcbond_other5.588
r_mcbond_it5.586
r_scbond_it5.554
r_scbond_other5.553
r_angle_other_deg2.38
r_angle_refined_deg1.6
r_symmetry_xyhbond_nbd_refined0.266
r_nbd_refined0.251
r_symmetry_nbd_other0.23
r_symmetry_nbd_refined0.226
r_nbd_other0.203
r_nbtor_refined0.184
r_xyhbond_nbd_refined0.182
r_xyhbond_nbd_other0.157
r_symmetry_xyhbond_nbd_other0.081
r_symmetry_nbtor_other0.076
r_chiral_restr0.063
r_bond_other_d0.034
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2703
Nucleic Acid Atoms
Solvent Atoms31
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing