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Crystal structure of Human Choline Kinase A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NW1 PDB entry 1NW1, residues 155-419 and 76-153
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 25% PEG3350, 0.1M Ammonium sulfate, 0.1M bis-Tris, pH 6.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.7 53.6 2.7 53.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.798 α = 90 b = 61.798 β = 90 c = 218.193 γ = 90
Symmetry Space Group P 43 21 2
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 2006-07-15 M SINGLE WAVELENGTH 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97625 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 1.85 50 96.7 0.051 12.9 9.6 36255
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) 1.85 1.92 72.6 0.691 2.4
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 1NW1, residues 155-419 and 76-153 1.9 30 34196 1751 99.05 0.231 0.2281 0.2785 0.2826 random 28.068
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] -0.046 -0.046 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.376 r_dihedral_angle_3_deg 13.972 r_dihedral_angle_4_deg 12.424 r_dihedral_angle_1_deg 5.942 r_scangle_it 3.972 r_mcangle_it 3.948 r_mcbond_it 2.977 r_scbond_it 2.889 r_angle_refined_deg 1.401 r_angle_other_deg 0.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.376 r_dihedral_angle_3_deg 13.972 r_dihedral_angle_4_deg 12.424 r_dihedral_angle_1_deg 5.942 r_scangle_it 3.972 r_mcangle_it 3.948 r_mcbond_it 2.977 r_scbond_it 2.889 r_angle_refined_deg 1.401 r_angle_other_deg 0.935 r_mcbond_other 0.798 r_symmetry_vdw_other 0.273 r_nbd_refined 0.214 r_nbd_other 0.189 r_nbtor_refined 0.185 r_symmetry_hbond_refined 0.163 r_xyhbond_nbd_refined 0.129 r_symmetry_vdw_refined 0.126 r_chiral_restr 0.087 r_nbtor_other 0.086 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2852 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ARP/wARP model building MolProbity model building