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Crystal structure of human ribokinase in complex with K+, Mg2+, and AMPCP
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 2.06 40.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.38 α = 90 b = 70.75 β = 92.36 c = 90.65 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 1.6 55.76 98.7 0.039 0.044 0.019 0.999 18.1 5 74579 23.511
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 1.6 1.63 94.1 0.66 0.737 0.435 0.714 2.2 2.2
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 1.6 55.756 74569 3798 98.649 0.154 0.1544 0.1528 0.1644 0.1847 0.1945 Random 28.841
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] -1.172 0.831 -1.044 2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.579 r_dihedral_angle_3_deg 12.65 r_lrange_it 6.338 r_lrange_other 6.234 r_dihedral_angle_1_deg 6.176 r_dihedral_angle_2_deg 6.084 r_scangle_it 3.908 r_scangle_other 3.907 r_scbond_it 2.595 r_scbond_other 2.594
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.579 r_dihedral_angle_3_deg 12.65 r_lrange_it 6.338 r_lrange_other 6.234 r_dihedral_angle_1_deg 6.176 r_dihedral_angle_2_deg 6.084 r_scangle_it 3.908 r_scangle_other 3.907 r_scbond_it 2.595 r_scbond_other 2.594 r_mcangle_it 2.196 r_mcangle_other 2.196 r_angle_refined_deg 1.681 r_mcbond_it 1.514 r_mcbond_other 1.507 r_angle_other_deg 0.575 r_symmetry_nbd_refined 0.245 r_nbd_refined 0.234 r_symmetry_xyhbond_nbd_refined 0.225 r_xyhbond_nbd_refined 0.221 r_nbd_other 0.206 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.172 r_ncsr_local_group_1 0.102 r_metal_ion_refined 0.099 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.08 r_dihedral_angle_other_2_deg 0.023 r_symmetry_xyhbond_nbd_other 0.017 r_bond_refined_d 0.009 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 4619 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling REFMAC phasing