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Crystal structure of Dephospho-CoA kinase (EC 2.7.1.24) (Dephosphocoenzyme A kinase) (tm1387) from THERMOTOGA MARITIMA at 2.60 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 5.2 293 30.0M NaCl, 32.5% PEG-8000, 0.1M Na,K-Phosphate pH 5.2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 42.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.832 α = 90 b = 87.217 β = 106.92 c = 98.586 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 CCD MAR CCD 165 mm 2003-07-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 0.97921, 0.9537246, 0.97907 APS 14-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.6 47.7 96.8 0.07 7.79 3.37 44701 40.15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 74.7 0.375 1.84
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-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.6 25.29 44609 2249 98.41 0.193 0.19328 0.191 0.245 0.2387 RANDOM 35.699
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] 0.66 1.01 -1.92 1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.132 r_dihedral_angle_3_deg 16.457 r_dihedral_angle_4_deg 15.29 r_scangle_it 6.649 r_dihedral_angle_1_deg 5.622 r_scbond_it 4.645 r_mcangle_it 2.158 r_angle_refined_deg 1.791 r_mcbond_it 1.742 r_angle_other_deg 0.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.132 r_dihedral_angle_3_deg 16.457 r_dihedral_angle_4_deg 15.29 r_scangle_it 6.649 r_dihedral_angle_1_deg 5.622 r_scbond_it 4.645 r_mcangle_it 2.158 r_angle_refined_deg 1.791 r_mcbond_it 1.742 r_angle_other_deg 0.899 r_mcbond_other 0.251 r_nbd_refined 0.229 r_symmetry_hbond_refined 0.186 r_nbd_other 0.177 r_nbtor_refined 0.176 r_symmetry_vdw_refined 0.158 r_symmetry_vdw_other 0.14 r_xyhbond_nbd_refined 0.133 r_nbtor_other 0.088 r_chiral_restr 0.085 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10846 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 572
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing