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CRYSTAL STRUCTURE OF DLK IN COMPLEX WITH COMPOUND 16
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 1.91 35.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.143 α = 90 b = 39.241 β = 104.4 c = 59.745 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 2016-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.95 32.48 99.8 0.17 0.203 0.11 0.978 4.5 3.3 18960
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 1.95 2 99.7 0.902 1.073 0.576 0.596 3.3
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 1.95 35 17948 1001 99.57 0.19882 0.1957 0.2055 0.25461 0.26 RANDOM 27.904
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] -1.13 0.08 -1.53 2.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.605 r_dihedral_angle_4_deg 16.059 r_dihedral_angle_3_deg 15.95 r_dihedral_angle_1_deg 6.163 r_long_range_B_refined 5.531 r_long_range_B_other 5.53 r_scangle_other 2.47 r_mcangle_it 1.913 r_mcangle_other 1.913 r_angle_refined_deg 1.885
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.605 r_dihedral_angle_4_deg 16.059 r_dihedral_angle_3_deg 15.95 r_dihedral_angle_1_deg 6.163 r_long_range_B_refined 5.531 r_long_range_B_other 5.53 r_scangle_other 2.47 r_mcangle_it 1.913 r_mcangle_other 1.913 r_angle_refined_deg 1.885 r_scbond_it 1.513 r_scbond_other 1.512 r_mcbond_it 1.158 r_mcbond_other 1.149 r_angle_other_deg 0.954 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2115 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 31
Software Software Software Name Purpose Aimless data scaling REFMAC refinement