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CRYSTAL STRUCTURE OF DLK IN COMPLEX WITH COMPOUND 19
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CEN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.7 291 20% PEG 3350, 0.2 M magnesium acetate, and 0.1 M HEPES/NaOH pH 7.5-7.9
Crystal Properties Matthews coefficient Solvent content 2.07 40.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.993 α = 90 b = 40.003 β = 108.54 c = 63.88 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2017-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 60.56 100 0.192 0.215 0.095 0.99 5.9 4.9 14397
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 100 1.033 1.16 0.521 0.644 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.2 60.56 13630 751 99.96 0.1832 0.17941 0.1885 0.2517 0.2571 RANDOM 33.94
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] -1.71 0.47 -1.18 2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.846 r_dihedral_angle_3_deg 14.847 r_dihedral_angle_4_deg 14.531 r_long_range_B_refined 7.516 r_long_range_B_other 7.516 r_dihedral_angle_1_deg 6.296 r_scangle_other 4.685 r_mcangle_other 3.695 r_mcangle_it 3.694 r_scbond_it 2.911
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.846 r_dihedral_angle_3_deg 14.847 r_dihedral_angle_4_deg 14.531 r_long_range_B_refined 7.516 r_long_range_B_other 7.516 r_dihedral_angle_1_deg 6.296 r_scangle_other 4.685 r_mcangle_other 3.695 r_mcangle_it 3.694 r_scbond_it 2.911 r_scbond_other 2.91 r_mcbond_it 2.406 r_mcbond_other 2.374 r_angle_refined_deg 1.751 r_angle_other_deg 1.082 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2123 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 33
Software Software Software Name Purpose Aimless data scaling REFMAC refinement