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Crystal structure of Zea mays adenosine kinase 3 (ZmADK3) in complex with AP5A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8RF7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 292 20% PEG8000, 0.5M LiCl, 0.1M Tris-HCl
Crystal Properties Matthews coefficient Solvent content 3.26 62.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.049 α = 90 b = 117.49 β = 90 c = 165.958 γ = 90
Symmetry Space Group I 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 16M 2023-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98012 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 2.261 47.946 89.8 0.2627 0.2751 0.0809 0.994 8.55 11.57 14056
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) 2.261 2.537 68.6 1.9552 2.0626 0.6475 0.652 1.43 9.93 703
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 2.261 47.95 14056 685 58.9 0.21 0.2076 0.1995 0.2566 0.2423 RANDOM 31.61
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] 5.5358 0.1173 -5.6531
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.15 t_omega_torsion 2.45 t_angle_deg 0.88 t_bond_d 0.007 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 2600 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 84
Software Software Software Name Purpose autoPROC data processing Aimless data scaling autoPROC data processing BUSTER refinement XDS data reduction PHASER phasing