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Crystal structure of human choline kinase beta in complex with phosphorylated hemicholinium-3 and adenosine nucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IG7 pdb entry 2ig7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 291 protein buffer: 0.01M Tris pH 8, 0.5M sodium chloride, 0.005M magnesium chloride, 0.01M DTT, 0.003M hemicholinium-3, 0.005M ADP; precipitant: 0.1M sodium cacodylate, 30% PEG-4000, 0.2M ammonium sulfate, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.24 45.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.994 α = 90 b = 72.987 β = 117.76 c = 62.397 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2008-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97243 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 1.3 30 97.6 0.04 14.4 3.6 92472
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) 1.3 1.35 82.4 0.559 2.4 7750
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 2ig7 1.302 28.296 92425 4612 97.405 0.16 0.158 0.1666 0.193 0.2025 RANDOM 14.43
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] 0.077 0.052 -0.128 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.734 r_dihedral_angle_4_deg 14.874 r_dihedral_angle_3_deg 12.047 r_sphericity_free 11.547 r_dihedral_angle_1_deg 5.381 r_sphericity_bonded 5.366 r_scangle_it 4.871 r_mcangle_it 3.72 r_scbond_it 3.667 r_mcbond_it 2.905
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.734 r_dihedral_angle_4_deg 14.874 r_dihedral_angle_3_deg 12.047 r_sphericity_free 11.547 r_dihedral_angle_1_deg 5.381 r_sphericity_bonded 5.366 r_scangle_it 4.871 r_mcangle_it 3.72 r_scbond_it 3.667 r_mcbond_it 2.905 r_rigid_bond_restr 2.25 r_angle_other_deg 1.881 r_mcbond_other 1.582 r_angle_refined_deg 1.462 r_chiral_restr 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2732 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 92
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling