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FrlB - Deglycase for 6-phosphofructose lysine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A3N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.1 M HEPES (pH 7.5) and 1.0 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.18 43.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.68 α = 90 b = 75.223 β = 90 c = 82.837 γ = 90
Symmetry Space Group P 21 21 2
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 R 200K-A 2018-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU MICROMAX-003 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.83 45.1 94.3 0.083 0.091 0.038 20.5 5.5 28584 11.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.88 84.7 0.462 0.511 0.214 3.7 5.2
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 2a3n 1.83 45.09 27187 1377 94.28 0.16209 0.16009 0.1716 0.20331 0.2102 RANDOM 16.357
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] -0.04 0.24 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.317 r_dihedral_angle_4_deg 19.011 r_dihedral_angle_3_deg 12.934 r_dihedral_angle_1_deg 6.65 r_long_range_B_refined 5.283 r_long_range_B_other 5.282 r_scangle_other 3.877 r_scbond_it 2.507 r_scbond_other 2.506 r_mcangle_other 2.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.317 r_dihedral_angle_4_deg 19.011 r_dihedral_angle_3_deg 12.934 r_dihedral_angle_1_deg 6.65 r_long_range_B_refined 5.283 r_long_range_B_other 5.282 r_scangle_other 3.877 r_scbond_it 2.507 r_scbond_other 2.506 r_mcangle_other 2.225 r_mcangle_it 2.223 r_angle_refined_deg 1.655 r_angle_other_deg 1.52 r_mcbond_it 1.507 r_mcbond_other 1.465 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 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 2510 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling MOLREP phasing