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Crystal structure of human choline kinase alpha in complex with hemicholinium-3
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 0.01M TRIS pH 8.0, 0.5M sodium chloride, 0.005M magnesium chloride, 0.01M DTT, 0.003M hemicholinium-3., pH 7.5, vapor diffusion, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.33 47.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.553 α = 90 b = 119.581 β = 90 c = 131.301 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 IMAGE PLATE RIGAKU RAXIS 2008-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.5418
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 2.35 30 100 0.113 9.9 6.6 37556
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) 2.35 2.43 100 0.971 6.3 3702
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 MR THROUGHOUT PDB ENTRY 2I7Q 2.35 29.801 37136 1072 99.715 0.222 0.221 0.2235 0.275 0.2768 THIN SHELLS (SFTOOLS) 36.43
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] -0.121 1.925 -1.804
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.794 r_dihedral_angle_4_deg 17.196 r_dihedral_angle_3_deg 14.225 r_dihedral_angle_1_deg 6.072 r_mcangle_it 3.672 r_scangle_it 3.507 r_scbond_it 2.457 r_mcbond_it 2.342 r_angle_refined_deg 1.399 r_angle_other_deg 0.889
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.794 r_dihedral_angle_4_deg 17.196 r_dihedral_angle_3_deg 14.225 r_dihedral_angle_1_deg 6.072 r_mcangle_it 3.672 r_scangle_it 3.507 r_scbond_it 2.457 r_mcbond_it 2.342 r_angle_refined_deg 1.399 r_angle_other_deg 0.889 r_mcbond_other 0.575 r_chiral_restr 0.08 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5335 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 64
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction Coot model building MolProbity model building