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Determination of potential scaffolds for human choline kinase alpha 1 by chemical deconvolution studies
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G15 PDB ENTRY 3G15
Crystallization Crystal Properties Matthews coefficient Solvent content 2.5 50.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.737 α = 90 b = 122.254 β = 90 c = 132.173 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 73 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 2.2 20 99.6 0.06 15 3.5 46439 2
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 2.2 2.32 98.7 0.53 2.6 3.5
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 3G15 2.2 20 45200 1189 99.41 0.20904 0.20778 0.2072 0.25764 0.2561 RANDOM 41.986
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] -2 3.84 -1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.123 r_dihedral_angle_4_deg 18.125 r_dihedral_angle_3_deg 17.547 r_dihedral_angle_1_deg 5.711 r_angle_refined_deg 1.428 r_chiral_restr 0.106 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.123 r_dihedral_angle_4_deg 18.125 r_dihedral_angle_3_deg 17.547 r_dihedral_angle_1_deg 5.711 r_angle_refined_deg 1.428 r_chiral_restr 0.106 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 5847 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling MOLREP phasing