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Crystal structure of dephospho-coenzyme A kinase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 PEG 3350, Bis-Tris (pH 6.5)
Crystal Properties Matthews coefficient Solvent content 2.26 45.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.246 α = 90 b = 58.246 β = 90 c = 105.137 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 PIXEL DECTRIS PILATUS 6M 2020-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0000 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 41.22 100 0.107 0.11 0.022 24.9 25.1 10444
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.22 0.372 0.38 0.075 11.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 2.15 41.22 10393 487 99.952 0.199 0.197 0.207 0.2333 0.245 1 36.619
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] -0.267 -0.267 0.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.401 r_dihedral_angle_3_deg 16.253 r_dihedral_angle_1_deg 8.109 r_lrange_it 7.658 r_lrange_other 7.658 r_scangle_it 5.79 r_scangle_other 5.787 r_dihedral_angle_2_deg 5.709 r_mcangle_it 4.602 r_mcangle_other 4.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.401 r_dihedral_angle_3_deg 16.253 r_dihedral_angle_1_deg 8.109 r_lrange_it 7.658 r_lrange_other 7.658 r_scangle_it 5.79 r_scangle_other 5.787 r_dihedral_angle_2_deg 5.709 r_mcangle_it 4.602 r_mcangle_other 4.6 r_scbond_it 3.711 r_scbond_other 3.708 r_mcbond_it 3.146 r_mcbond_other 3.144 r_angle_refined_deg 0.621 r_symmetry_xyhbond_nbd_refined 0.258 r_symmetry_nbd_other 0.228 r_nbd_other 0.22 r_nbd_refined 0.217 r_angle_other_deg 0.203 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.151 r_symmetry_nbd_refined 0.122 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.071 r_chiral_restr 0.032 r_gen_planes_refined 0.005 r_bond_refined_d 0.003 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1326 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling SHARP phasing