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Dipeptide Gly-Pro binds to a glycolytic enzyme fructose bisphosphate aldolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KY6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Lithium Sulfate, 0.1 M Bis-Tris pH 6.2 and 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.3 46.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.567 α = 79.95 b = 67.636 β = 73.13 c = 88.908 γ = 65.58
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 PILATUS 6M-F 2018-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.072 ESRF ID29
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 1.9 48.37 83.45 0.178 0.2 0.09 0.992 7.04 4.9 88957
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 1.9 2.04 1.194 1.34 0.6 0.623
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 5KY6 1.9 48.37 73398 3860 71.13 0.21631 0.21435 0.2277 0.25381 0.2652 RANDOM 20.153
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] 0.08 -0.21 0.03 0.11 0.04 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.96 r_dihedral_angle_4_deg 24.257 r_dihedral_angle_3_deg 17.854 r_dihedral_angle_1_deg 6.603 r_long_range_B_refined 3.604 r_long_range_B_other 3.462 r_angle_refined_deg 1.566 r_mcangle_it 1.296 r_mcangle_other 1.296 r_angle_other_deg 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.96 r_dihedral_angle_4_deg 24.257 r_dihedral_angle_3_deg 17.854 r_dihedral_angle_1_deg 6.603 r_long_range_B_refined 3.604 r_long_range_B_other 3.462 r_angle_refined_deg 1.566 r_mcangle_it 1.296 r_mcangle_other 1.296 r_angle_other_deg 0.98 r_scangle_other 0.883 r_mcbond_it 0.715 r_mcbond_other 0.714 r_scbond_it 0.622 r_scbond_other 0.488 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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 10156 Nucleic Acid Atoms Solvent Atoms 614 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing