6TMP | pdb_00006tmp

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
3.2361.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.292α = 90
b = 109.292β = 90
c = 83.654γ = 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
12.07694.6593.90.092116.810.219985
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)
12.0762.34476.21.1970.7471.99.2

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-VALUE2.07694.651998493455.1280.1750.17190.180.24010.2447.262
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]
0.080.040.08-0.259
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.121
r_dihedral_angle_4_deg21.312
r_dihedral_angle_3_deg18.963
r_lrange_other9.718
r_lrange_it9.704
r_dihedral_angle_1_deg7.586
r_scangle_it7.291
r_scangle_other7.289
r_mcangle_other6.369
r_mcangle_it6.361
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.121
r_dihedral_angle_4_deg21.312
r_dihedral_angle_3_deg18.963
r_lrange_other9.718
r_lrange_it9.704
r_dihedral_angle_1_deg7.586
r_scangle_it7.291
r_scangle_other7.289
r_mcangle_other6.369
r_mcangle_it6.361
r_scbond_it4.712
r_scbond_other4.71
r_mcbond_it4.307
r_mcbond_other4.289
r_angle_other_deg2.406
r_angle_refined_deg1.617
r_nbd_other0.263
r_nbd_refined0.228
r_symmetry_nbd_other0.225
r_symmetry_nbd_refined0.209
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.168
r_symmetry_xyhbond_nbd_refined0.108
r_symmetry_xyhbond_nbd_other0.098
r_symmetry_nbtor_other0.075
r_chiral_restr0.073
r_bond_other_d0.034
r_bond_refined_d0.01
r_gen_planes_other0.009
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2766
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing