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Frutapin complexed with alpha-D-glucose
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 monobasic phosphate, 20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.17 43.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.023 α = 90 b = 74.023 β = 90 c = 185.522 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 1.6 185.52 100 0.205 0.995 9.3 19.3 78721
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 1.6 1.63 100 0.2018 0.594 1.9 19.5
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 1.6 64.11 74711 3914 99.98 0.15118 0.14907 0.1588 0.1918 0.2018 RANDOM 21.597
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] -0.02 -0.01 -0.02 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.07 r_dihedral_angle_3_deg 16.215 r_dihedral_angle_4_deg 16.01 r_dihedral_angle_1_deg 9.001 r_long_range_B_refined 5.039 r_long_range_B_other 4.99 r_scangle_other 3.16 r_angle_refined_deg 2.903 r_mcangle_it 2.598 r_mcangle_other 2.598
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.07 r_dihedral_angle_3_deg 16.215 r_dihedral_angle_4_deg 16.01 r_dihedral_angle_1_deg 9.001 r_long_range_B_refined 5.039 r_long_range_B_other 4.99 r_scangle_other 3.16 r_angle_refined_deg 2.903 r_mcangle_it 2.598 r_mcangle_other 2.598 r_scbond_it 2.155 r_scbond_other 2.155 r_mcbond_it 1.773 r_mcbond_other 1.773 r_angle_other_deg 1.339 r_chiral_restr 0.187 r_bond_refined_d 0.033 r_gen_planes_refined 0.017 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 417 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement DIALS data scaling DIALS data reduction Aimless data scaling PHASER phasing