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Crystal structure of human ribokinase in complex with K+, Mg2+, and AMPPNP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277.15 0.1 M TrisHCl (pH 8.5), 25% (W/V) PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.08 40.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.41 α = 90 b = 70.93 β = 92.49 c = 90.92 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 PILATUS3 S 6M 2018-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
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 1.45 70.93 99.6 0.048 0.054 0.024 0.999 13.9 4.8 101613 20.117
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 1.45 1.48 96.9 0.632 0.716 0.329 0.67 1.8 4.3
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-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 1.45 55.967 101588 5067 99.534 0.132 0.1319 0.1296 0.1295 0.1763 0.1768 Random 24.795
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] -1.261 0.457 0.077 1.139
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 16.093 r_dihedral_angle_6_deg 15.833 r_lrange_other 15.197 r_scangle_it 12.346 r_scangle_other 12.344 r_dihedral_angle_3_deg 11.999 r_mcangle_other 9.367 r_mcangle_it 9.365 r_scbond_it 8.85 r_scbond_other 8.849
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 16.093 r_dihedral_angle_6_deg 15.833 r_lrange_other 15.197 r_scangle_it 12.346 r_scangle_other 12.344 r_dihedral_angle_3_deg 11.999 r_mcangle_other 9.367 r_mcangle_it 9.365 r_scbond_it 8.85 r_scbond_other 8.849 r_dihedral_angle_2_deg 8.354 r_mcbond_it 6.935 r_mcbond_other 6.91 r_dihedral_angle_1_deg 5.886 r_rigid_bond_restr 3.775 r_angle_refined_deg 1.655 r_angle_other_deg 0.581 r_nbd_refined 0.233 r_symmetry_nbd_other 0.195 r_nbd_other 0.187 r_xyhbond_nbd_refined 0.185 r_symmetry_nbd_refined 0.179 r_nbtor_refined 0.174 r_ncsr_local_group_1 0.105 r_symmetry_xyhbond_nbd_refined 0.104 r_chiral_restr 0.091 r_symmetry_xyhbond_nbd_other 0.09 r_symmetry_nbtor_other 0.08 r_metal_ion_refined 0.078 r_chiral_restr_other 0.074 r_dihedral_angle_other_2_deg 0.013 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4608 Nucleic Acid Atoms Solvent Atoms 582 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling REFMAC phasing