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Structure of maize adenosine kinase 2 (ADK2) in complex with AMP-PCP
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 5.5 292 Ammonium sulfate/Sodium fluoride/Sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.32 46.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.85 α = 90 b = 135.85 β = 90 c = 78.634 γ = 90
Symmetry Space Group P 4 21 2
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 2022-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98011 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 2.359 96.06 93.7 0.3139 0.3202 0.0628 0.997 12.42 25.61 20930
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) 2.359 2.506 78.9 2.8558 2.9108 0.5593 0.511 1.48 26.8 1046
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 FOURIER SYNTHESIS THROUGHOUT 2.359 96.06 20930 1045 67.7 0.2609 0.2601 0.2433 0.2779 0.2691 RANDOM 55.62
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] -9.3516 -9.3516 18.7032
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.8 t_omega_torsion 2.31 t_angle_deg 0.88 t_bond_d 0.007 t_dihedral_angle_d t_gen_planes t_it t_nbd t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5123 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 72
Software Software Software Name Purpose autoPROC data processing autoPROC data processing Aimless data scaling autoPROC data processing BUSTER refinement autoPROC data reduction FFT phasing