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Crystal structure of the arginine kinase Der p 20_like (putative isoform)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 293 0.05 M Calcium chloride dihydrate, 0.1 M BIS-TRIS pH 6.5, 30% v/v Polyethylene glycol monomethyl ether 550
Crystal Properties Matthews coefficient Solvent content 2.28 46.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.561 α = 90 b = 61.894 β = 96.442 c = 61.769 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 X 16M 2020-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.978564 PETRA III, DESY P11
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 1.8 48.25 97.9 0.086 0.119 0.081 0.988 6.4 3.2 33156
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 1.8 1.84 0.427 0.582 0.393 0.857 3.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 48.25 33139 1594 97.923 0.187 0.1847 0.1847 0.2252 0.2252 37.66
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] -1.851 -1.743 3.346 -1.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.594 r_dihedral_angle_2_deg 15.805 r_dihedral_angle_3_deg 15.16 r_lrange_it 7.609 r_lrange_other 7.573 r_dihedral_angle_1_deg 6.645 r_scangle_it 4.186 r_scangle_other 4.185 r_mcangle_other 2.911 r_mcangle_it 2.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.594 r_dihedral_angle_2_deg 15.805 r_dihedral_angle_3_deg 15.16 r_lrange_it 7.609 r_lrange_other 7.573 r_dihedral_angle_1_deg 6.645 r_scangle_it 4.186 r_scangle_other 4.185 r_mcangle_other 2.911 r_mcangle_it 2.91 r_scbond_it 2.705 r_scbond_other 2.703 r_mcbond_it 1.93 r_mcbond_other 1.929 r_angle_refined_deg 1.451 r_angle_other_deg 0.48 r_symmetry_nbd_refined 0.381 r_symmetry_xyhbond_nbd_refined 0.337 r_symmetry_xyhbond_nbd_other 0.249 r_xyhbond_nbd_refined 0.238 r_nbd_refined 0.224 r_nbd_other 0.211 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.176 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2779 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing