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Crystal structure of human Choline Kinase A in complex with UNC0638
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EQP 5EQP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.5 294 22.5% PEG smear low molecular weight, 0.1M MES pH 6.5, 10% 2-propanol
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.033 α = 90 b = 132.033 β = 90 c = 168.988 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2018-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976250 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.66 48.45 93.6 0.06 0.065 24.8 10.8 165115
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) Redundancy Number Unique Reflections (All) 1 1.66 1.69 0.422 0.456 5.8 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5EQP 2.4 48.45 55873 3035 99.97 0.18072 0.17854 0.1859 0.22085 0.2248 RANDOM 54.478
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 -0.32 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.113 r_long_range_B_refined 11.028 r_long_range_B_other 11.028 r_dihedral_angle_2_deg 9.353 r_scangle_other 8.67 r_mcangle_it 7.528 r_mcangle_other 7.527 r_dihedral_angle_1_deg 6.763 r_scbond_it 6.469 r_scbond_other 6.418
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.113 r_long_range_B_refined 11.028 r_long_range_B_other 11.028 r_dihedral_angle_2_deg 9.353 r_scangle_other 8.67 r_mcangle_it 7.528 r_mcangle_other 7.527 r_dihedral_angle_1_deg 6.763 r_scbond_it 6.469 r_scbond_other 6.418 r_mcbond_it 5.479 r_mcbond_other 5.479 r_angle_refined_deg 1.697 r_angle_other_deg 1.234 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.004 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 5883 Nucleic Acid Atoms Solvent Atoms 396 Heterogen Atoms 169
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing autoPROC data reduction