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Crystal structure of human ribokinase in complex with AMPCP
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 295.15 0.2 M sodium acetate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.15 42.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.11 α = 90 b = 71.86 β = 91.78 c = 91.43 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 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 1.8 56.49 99.21 0.054 0.06 0.027 0.999 14.5 4.8 54971 26.68
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 1.8 1.83 97.7 0.538 0.605 0.271 0.855 2.3 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 5C40 1.8 56.49 52215 2738 99.18 0.15384 0.15218 0.1628 0.18632 0.1965 RANDOM 34.356
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] 0.1 1.61 -0.88 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.604 r_dihedral_angle_4_deg 20.297 r_dihedral_angle_3_deg 13.635 r_long_range_B_refined 6.746 r_long_range_B_other 6.644 r_dihedral_angle_1_deg 6.637 r_scangle_other 2.651 r_angle_refined_deg 1.824 r_scbond_other 1.809 r_scbond_it 1.808
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.604 r_dihedral_angle_4_deg 20.297 r_dihedral_angle_3_deg 13.635 r_long_range_B_refined 6.746 r_long_range_B_other 6.644 r_dihedral_angle_1_deg 6.637 r_scangle_other 2.651 r_angle_refined_deg 1.824 r_scbond_other 1.809 r_scbond_it 1.808 r_mcangle_it 1.656 r_mcangle_other 1.656 r_angle_other_deg 1.524 r_mcbond_it 1.113 r_mcbond_other 1.113 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4610 Nucleic Acid Atoms Solvent Atoms 454 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing