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Structure of Rhizopus azygosporus Kinase in complex with GDP and MG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A0A367K070-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 0.2 M NH4Cl, 20% (w/v) PEG-3350, PEG 400
Crystal Properties Matthews coefficient Solvent content 2.38 48.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.417 α = 90 b = 66.46 β = 90 c = 73.703 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 EIGER2 S 16M M 2024-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.9793 NSLS-II 17-ID-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 1.65 34.76 100 0.15 0.157 0.044 0.998 10 12.5 26297
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 100 4.708 1.388 0.375 12.3
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 1.65 30 22793 1181 99.95 0.17256 0.16941 0.1823 0.23727 0.2434 RANDOM 31.587
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] -2.54 -0.23 2.77
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 20.955 r_long_range_B_other 19.981 r_scangle_other 14.539 r_dihedral_angle_3_deg 13.342 r_mcangle_it 12.28 r_mcangle_other 12.278 r_scbond_it 10.05 r_scbond_other 10.042 r_mcbond_it 8.728 r_mcbond_other 8.613
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 20.955 r_long_range_B_other 19.981 r_scangle_other 14.539 r_dihedral_angle_3_deg 13.342 r_mcangle_it 12.28 r_mcangle_other 12.278 r_scbond_it 10.05 r_scbond_other 10.042 r_mcbond_it 8.728 r_mcbond_other 8.613 r_dihedral_angle_2_deg 7.34 r_dihedral_angle_1_deg 6.548 r_rigid_bond_restr 4.019 r_angle_refined_deg 1.648 r_angle_other_deg 0.593 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1355 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing