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Crystal structure of the arginine kinase Der p 20.0101
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 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.18 43.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.28 α = 90 b = 99.02 β = 108.056 c = 77.883 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 Bruker PHOTON III 2022-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE Excillum MetalJet D2+ 70 kV 1.34138
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 59.3 90.8 0.144 0.978 4.3 2.9 49720
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 0.5 0.708
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 1.9 59.3 40075 2044 73.106 0.272 0.2697 0.2695 0.3098 0.3099 7.484
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] 0.213 -0.444 1.494 -1.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.146 r_dihedral_angle_3_deg 14.45 r_dihedral_angle_2_deg 6.974 r_dihedral_angle_1_deg 6.679 r_angle_refined_deg 1.232 r_lrange_it 1.087 r_lrange_other 1.059 r_scangle_it 0.592 r_scangle_other 0.592 r_mcangle_it 0.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.146 r_dihedral_angle_3_deg 14.45 r_dihedral_angle_2_deg 6.974 r_dihedral_angle_1_deg 6.679 r_angle_refined_deg 1.232 r_lrange_it 1.087 r_lrange_other 1.059 r_scangle_it 0.592 r_scangle_other 0.592 r_mcangle_it 0.586 r_mcangle_other 0.586 r_angle_other_deg 0.425 r_mcbond_it 0.409 r_mcbond_other 0.409 r_scbond_it 0.394 r_scbond_other 0.394 r_symmetry_xyhbond_nbd_refined 0.35 r_nbd_other 0.244 r_xyhbond_nbd_refined 0.243 r_symmetry_nbd_refined 0.221 r_nbd_refined 0.22 r_symmetry_nbd_other 0.207 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_other 0.151 r_ncsr_local_group_1 0.088 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5580 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing