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Crystal structure of Human Choline Kinase alpha 2 in complex with Phosphocholine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NW1 PDB ENTRY 1NW1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.01 M MGCL2, 15% PEG 3350, 0.2 M NAF., pH 7.50
Crystal Properties Matthews coefficient Solvent content 3.64 65.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.5 α = 90 b = 128.3 β = 90 c = 172.2 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 CCD MARRESEARCH 2005-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
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 2.4 15 99.8 0.11 13.9 8.1 46369
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 2.4 2.5 99.1 0.57 3.2 6.1
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 PDB ENTRY 1NW1 2.4 15 41524 4638 99.9 0.219 0.214 0.2127 0.259 0.2577 RANDOM 35.66
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] 1.26 -2.86 1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.536 r_dihedral_angle_3_deg 16.955 r_dihedral_angle_4_deg 16.331 r_dihedral_angle_1_deg 5.811 r_scangle_it 2.014 r_scbond_it 1.226 r_angle_refined_deg 1.225 r_mcangle_it 0.974 r_mcbond_it 0.568 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.536 r_dihedral_angle_3_deg 16.955 r_dihedral_angle_4_deg 16.331 r_dihedral_angle_1_deg 5.811 r_scangle_it 2.014 r_scbond_it 1.226 r_angle_refined_deg 1.225 r_mcangle_it 0.974 r_mcbond_it 0.568 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.214 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.085 r_symmetry_hbond_refined 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5534 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction MOLREP phasing