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Crystal structure of dephospho-coenzyme A kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8JVF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 PEG 3350, coenzyme A, sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.44 49.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.143 α = 90 b = 89.143 β = 90 c = 83.886 γ = 120
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 EIGER X 4M 2020-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.0000 Photon Factory BL-1A
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 2.5 44.611 100 0.052 0.053 0.011 42.1 20.9 13215
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 2.5 2.6 0.383 0.392 0.085 8.8
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.5 44.611 13184 682 99.962 0.209 0.2059 0.2134 0.2735 0.281 1 51.621
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] -0.181 -0.09 -0.181 0.587
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.248 r_dihedral_angle_3_deg 15.746 r_lrange_it 9.675 r_lrange_other 9.674 r_dihedral_angle_1_deg 8.038 r_scangle_it 7.44 r_scangle_other 7.438 r_dihedral_angle_2_deg 6.618 r_mcangle_it 5.872 r_mcangle_other 5.871
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.248 r_dihedral_angle_3_deg 15.746 r_lrange_it 9.675 r_lrange_other 9.674 r_dihedral_angle_1_deg 8.038 r_scangle_it 7.44 r_scangle_other 7.438 r_dihedral_angle_2_deg 6.618 r_mcangle_it 5.872 r_mcangle_other 5.871 r_scbond_it 4.758 r_scbond_other 4.756 r_mcbond_it 3.975 r_mcbond_other 3.973 r_angle_refined_deg 0.474 r_nbd_other 0.27 r_symmetry_nbd_other 0.237 r_nbd_refined 0.224 r_symmetry_xyhbond_nbd_refined 0.21 r_nbtor_refined 0.174 r_angle_other_deg 0.163 r_symmetry_nbd_refined 0.16 r_xyhbond_nbd_refined 0.144 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.024 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_refined_d 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2504 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing