8BI6

Crystal structure of human Choline Kinase A in complex with UNC0638


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION6.529422.5% PEG smear low molecular weight, 0.1M MES pH 6.5, 10% 2-propanol

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.033α = 90
b = 132.033β = 90
c = 168.988γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976250DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.6648.4593.60.060.06524.810.8165115
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.661.690.4220.4565.82.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5EQP2.448.4555873303599.970.180720.178540.22085RANDOM54.478
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]
-0.32-0.320.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.113
r_long_range_B_refined11.028
r_long_range_B_other11.028
r_dihedral_angle_2_deg9.353
r_scangle_other8.67
r_mcangle_it7.528
r_mcangle_other7.527
r_dihedral_angle_1_deg6.763
r_scbond_it6.469
r_scbond_other6.418
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.113
r_long_range_B_refined11.028
r_long_range_B_other11.028
r_dihedral_angle_2_deg9.353
r_scangle_other8.67
r_mcangle_it7.528
r_mcangle_other7.527
r_dihedral_angle_1_deg6.763
r_scbond_it6.469
r_scbond_other6.418
r_mcbond_it5.479
r_mcbond_other5.479
r_angle_refined_deg1.697
r_angle_other_deg1.234
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_bond_other_d0.004
r_gen_planes_other0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5883
Nucleic Acid Atoms
Solvent Atoms396
Heterogen Atoms169

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
autoPROCdata reduction