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Crystal structure of adenosine 5'-phosphosulfate kinase from Archaeoglobus fulgidus in complex with AMP-PNP and APS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CB6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 1.0 M Sodium citrate tribasic, 0.1 M Sodium cacodylate-hydrochloric acid
Crystal Properties Matthews coefficient Solvent content 3.44 64.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.23 α = 90 b = 238.24 β = 93.38 c = 132.47 γ = 90
Symmetry Space Group C 1 2 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 PILATUS3 6M 2021-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.91 50 98.3 0.987 6 4.3 122344
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.91 2.03 0.587
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5CB6 1.91 48.48 1.37 122311 1998 98.29 0.2146 0.214 0.2144 0.2463 0.2463
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.041 f_angle_d 0.944 f_chiral_restr 0.052 f_plane_restr 0.007 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8370 Nucleic Acid Atoms Solvent Atoms 939 Heterogen Atoms 402
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing