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Crystal structure of Human Choline Kinase alpha 2
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, 0.2M NAF, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.66 53.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.18 α = 90 b = 122.82 β = 90 c = 132.17 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 ADSC CCD 2005-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 CHESS A1
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 2.15 30 99.9 0.11 20.38 17.9 50560
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 2.15 2.25 100 0.62 5.76 17.9
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 2.15 30 45480 5080 100 0.204 0.199 0.1994 0.256 0.2554 RANDOM 35.96
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] -1.31 2.01 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.366 r_dihedral_angle_4_deg 18.464 r_dihedral_angle_3_deg 16.103 r_dihedral_angle_1_deg 5.583 r_scangle_it 3.077 r_scbond_it 2.066 r_mcangle_it 1.418 r_angle_refined_deg 1.371 r_mcbond_it 0.885 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.366 r_dihedral_angle_4_deg 18.464 r_dihedral_angle_3_deg 16.103 r_dihedral_angle_1_deg 5.583 r_scangle_it 3.077 r_scbond_it 2.066 r_mcangle_it 1.418 r_angle_refined_deg 1.371 r_mcbond_it 0.885 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.185 r_symmetry_hbond_refined 0.156 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 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 5686 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing