☰ Navigation Tabs
A ternary complex of plant adenosine kinase 1 from moss Physcomitrella patens (PpADK1) with adenosine and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8RPA Adenosine kinase 3 from Zea mays
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 37.5% MPD/PEG1000/PEG3350 + 0.1M Carboxylic acids (Sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, potassium sodium tartrate tetrahydrate, sodium oxamate) + 0.1M MES/Imidazole pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.98 37.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.59 α = 90 b = 93.083 β = 90 c = 131.671 γ = 90
Symmetry Space Group P 21 21 21
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 9M 2024-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.987 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.73 76.008 93.1 0.3146 0.3288 0.0948 0.984 6.12 11.89 37232
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.73 1.934 82.2 2.3345 2.4325 0.6775 0.61 1.68 12.59 1862
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.73 24.41 37199 1819 56.6 0.2219 0.2201 0.2131 0.2552 0.2429 RANDOM 30.31
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] 10.4975 -6.9439 -3.5536
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.16 t_omega_torsion 3.54 t_angle_deg 1 t_bond_d 0.009 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5112 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 102
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling STARANISO data scaling BUSTER refinement PHASER phasing