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Frutapin complexed with alpha-D-mannose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KRP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 277 0.04 M Potassium phosphate monobasic, 16% PEG 8000,
Crystal Properties Matthews coefficient Solvent content 2.17 43.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.956 α = 90 b = 73.956 β = 90 c = 185.238 γ = 120
Symmetry Space Group P 31 2 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 PILATUS 6M-F 2016-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96859 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 185.24 100 0.133 0.992 8.8 6.3 65624
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 99.9 0.907 0.614 2.1 6.3
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 FREE R-VALUE 5krp 1.7 64.05 62206 3343 99.98 0.1436 0.14104 0.1526 0.19083 0.2002 RANDOM 20.775
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] -4.55 -4.55 9.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.294 r_dihedral_angle_4_deg 16.521 r_dihedral_angle_3_deg 15.2 r_dihedral_angle_1_deg 7.899 r_long_range_B_refined 6.653 r_long_range_B_other 6.574 r_scangle_other 4.793 r_mcangle_it 3.511 r_mcangle_other 3.511 r_scbond_it 3.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.294 r_dihedral_angle_4_deg 16.521 r_dihedral_angle_3_deg 15.2 r_dihedral_angle_1_deg 7.899 r_long_range_B_refined 6.653 r_long_range_B_other 6.574 r_scangle_other 4.793 r_mcangle_it 3.511 r_mcangle_other 3.511 r_scbond_it 3.271 r_scbond_other 3.27 r_angle_refined_deg 2.477 r_mcbond_it 2.419 r_mcbond_other 2.418 r_angle_other_deg 1.175 r_chiral_restr 0.147 r_bond_refined_d 0.026 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 4608 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing