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Crystal structure of the arginine kinase Sar s 20
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 Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.42 49.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.476 α = 90 b = 80.904 β = 90 c = 100.504 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 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 1.4 48.48 99 0.066 0.079 0.042 0.999 13.8 6.5 77680
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 1.4 1.42 1.244 1.462 0.763 0.572 6.8
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 1.4 43.662 77614 3925 98.776 0.165 0.1639 0.1639 0.1939 0.1939 18.46
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] -0.424 0.832 -0.408
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.765 r_dihedral_angle_3_deg 14.598 r_lrange_it 9.212 r_lrange_other 8.348 r_dihedral_angle_2_deg 8.007 r_dihedral_angle_1_deg 6.302 r_scangle_it 4.442 r_scangle_other 4.441 r_scbond_it 2.871 r_scbond_other 2.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.765 r_dihedral_angle_3_deg 14.598 r_lrange_it 9.212 r_lrange_other 8.348 r_dihedral_angle_2_deg 8.007 r_dihedral_angle_1_deg 6.302 r_scangle_it 4.442 r_scangle_other 4.441 r_scbond_it 2.871 r_scbond_other 2.87 r_mcangle_it 2.264 r_mcangle_other 2.264 r_angle_refined_deg 1.805 r_mcbond_it 1.489 r_mcbond_other 1.489 r_angle_other_deg 0.57 r_xyhbond_nbd_refined 0.304 r_symmetry_xyhbond_nbd_refined 0.294 r_symmetry_nbd_refined 0.232 r_nbd_refined 0.23 r_nbd_other 0.21 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.186 r_symmetry_xyhbond_nbd_other 0.178 r_xyhbond_nbd_other 0.14 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2797 Nucleic Acid Atoms Solvent Atoms 655 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing