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Crystal structure of dephospho-coenzyme A kinase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 1500, GTP
Crystal Properties Matthews coefficient Solvent content 2.36 47.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.101 α = 90 b = 55.101 β = 90 c = 122.584 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 2.4 50 100 0.073 0.075 0.015 30.7 24.4 7963
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 2.4 2.49 100 0.417 0.425 0.082 10.7 26.5
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 2.4 41.01 7916 399 99.987 0.22 0.2185 0.2245 0.2578 0.2667 1 59.86
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] 2.62 2.62 -5.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.877 r_dihedral_angle_3_deg 15.721 r_lrange_it 12.903 r_lrange_other 12.903 r_scangle_it 10.158 r_scangle_other 10.152 r_mcangle_it 7.919 r_dihedral_angle_1_deg 7.918 r_mcangle_other 7.915 r_scbond_it 6.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.877 r_dihedral_angle_3_deg 15.721 r_lrange_it 12.903 r_lrange_other 12.903 r_scangle_it 10.158 r_scangle_other 10.152 r_mcangle_it 7.919 r_dihedral_angle_1_deg 7.918 r_mcangle_other 7.915 r_scbond_it 6.773 r_scbond_other 6.769 r_dihedral_angle_2_deg 6.528 r_mcbond_it 5.416 r_mcbond_other 5.411 r_angle_refined_deg 0.722 r_dihedral_angle_other_2_deg 0.585 r_nbd_other 0.27 r_angle_other_deg 0.24 r_symmetry_nbd_other 0.237 r_nbd_refined 0.223 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.168 r_xyhbond_nbd_refined 0.149 r_symmetry_nbd_refined 0.129 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.035 r_gen_planes_refined 0.01 r_bond_refined_d 0.002 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 993 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling SHARP phasing