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Crystal structure of human ribokinase in complex with K+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C40
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 2.09 41.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.56 α = 90 b = 70.87 β = 93.06 c = 91.12 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 55.95 99.7 0.046 0.051 0.023 0.999 15.5 4.9 102166 18.379
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 99.7 0.651 0.728 0.32 0.741 2.3 4.9
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 MOLECULAR REPLACEMENT THROUGHOUT 1.45 55.912 102148 5096 99.681 0.149 0.1491 0.1471 0.1466 0.1891 0.1897 Random 23.818
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] 2.365 0.833 -1.822 -0.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.997 r_dihedral_angle_6_deg 15.97 r_lrange_it 14.735 r_lrange_other 14.019 r_dihedral_angle_3_deg 12.31 r_scangle_it 11.499 r_scangle_other 11.498 r_mcangle_other 9.353 r_mcangle_it 9.351 r_scbond_it 8.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.997 r_dihedral_angle_6_deg 15.97 r_lrange_it 14.735 r_lrange_other 14.019 r_dihedral_angle_3_deg 12.31 r_scangle_it 11.499 r_scangle_other 11.498 r_mcangle_other 9.353 r_mcangle_it 9.351 r_scbond_it 8.31 r_scbond_other 8.308 r_mcbond_it 7.146 r_mcbond_other 7.142 r_dihedral_angle_1_deg 6.408 r_rigid_bond_restr 5.379 r_angle_refined_deg 1.743 r_angle_other_deg 0.619 r_nbd_refined 0.236 r_nbd_other 0.225 r_symmetry_nbd_other 0.196 r_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.161 r_xyhbond_nbd_other 0.119 r_metal_ion_refined 0.107 r_ncsr_local_group_1 0.106 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.034 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4607 Nucleic Acid Atoms Solvent Atoms 635 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling PHASER phasing