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Crystal structure of human choline kinase alpha in complex with hemicholinium-3 and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I7Q PDB ENTRY 2I7Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 25% PEG-3350, 0.2M lithium sulfate, 0.1M HEPES. Crystallization sample buffer: 0.01M TRIS pH 8.0, 0.5M sodium chloride, 0.005M magnesium chloride, 0.01M DTT, 0.003M hemicholinium-3, 0.005M ADP., vapor diffusion, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.32 47.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.802 α = 90 b = 118.986 β = 90 c = 131.039 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 300 mm plate 2008-02-14 SINGLE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.96863 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 50 97 0.069 11.4 6.5 93657
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.76 75.6 0.797 2.6 7162
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 PDB ENTRY 2I7Q 1.7 30 93409 2122 96.694 0.221 0.22 0.2224 0.257 0.2556 thin shells (sftools) 22.163
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] -0.522 1.292 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.119 r_dihedral_angle_4_deg 13.077 r_dihedral_angle_3_deg 12.758 r_dihedral_angle_1_deg 5.454 r_scangle_it 3.479 r_mcangle_it 2.992 r_scbond_it 2.41 r_angle_other_deg 2.189 r_mcbond_it 2.012 r_angle_refined_deg 1.388
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.119 r_dihedral_angle_4_deg 13.077 r_dihedral_angle_3_deg 12.758 r_dihedral_angle_1_deg 5.454 r_scangle_it 3.479 r_mcangle_it 2.992 r_scbond_it 2.41 r_angle_other_deg 2.189 r_mcbond_it 2.012 r_angle_refined_deg 1.388 r_mcbond_other 0.586 r_chiral_restr 0.083 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5354 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 149
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Coot model building MolProbity model building ARP/wARP model building