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Crystal structure of E. coli SF kinase (YihV) in complex with product sulfofructose phosphate (SFP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AG6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 25% PEG 1500 w/v, 0.1 M PCTP buffer pH8 (propionic acid, cacodylate, bistris propane)
Crystal Properties Matthews coefficient Solvent content 2.6 52.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.548 α = 90 b = 91.856 β = 90 c = 312.142 γ = 90
Symmetry Space Group P 2 21 21
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 EIGER2 XE 16M 2019-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
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 2.97 79.16 100 0.19 0.203 0.071 0.916 7 8.1 29364
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 2.97 3.15 100 1.342 1.43 0.489 0.841 8.2
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 7AG6 2.97 79.01 27821 1471 99.96 0.2343 0.2317 0.2312 0.2844 0.2775 RANDOM 67.685
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] -2.1 9.13 -7.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.585 r_dihedral_angle_4_deg 22.792 r_dihedral_angle_3_deg 17.156 r_dihedral_angle_1_deg 6.206 r_angle_refined_deg 1.472 r_angle_other_deg 1.318 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.585 r_dihedral_angle_4_deg 22.792 r_dihedral_angle_3_deg 17.156 r_dihedral_angle_1_deg 6.206 r_angle_refined_deg 1.472 r_angle_other_deg 1.318 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8088 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction xia2 data reduction MOLREP phasing