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Crystal structure of Triosephosphate isomerase from Stenotrophomonas maltophilia K279a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IOT PDB entry 4iot as per MORDA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 290 RigakuReagents JCSG+ screen, condition A9: 200mM Ammonium chloride, 20% (w/V) PEG 3350: StmaA.00317.a.B1.PW38736 at 25.5mg/ml + 5mM Glucose-3-phosphate : cryo: 20% EG + 5mM glucose-3-phosphate, tray 313955a9: puck pzy9-10.
Crystal Properties Matthews coefficient Solvent content 2.14 42.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.5 α = 71.9 b = 46.66 β = 71.086 c = 66.83 γ = 68.356
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 2020-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.7 50 97 0.037 0.043 0.999 19.17 3.898 48225 34.952
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 95.6 0.485 0.561 0.876 3.3 3.976
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB entry 4iot as per MORDA 1.7 39.28 1.99 48219 1964 97.13 0.1697 0.1679 0.1687 0.2149 0.2126 0 39.1
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.2076 f_angle_d 0.8788 f_chiral_restr 0.0561 f_bond_d 0.0077 f_plane_restr 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3684 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 4
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing Coot model building