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Crystal Structure of Fructose-1,6-bisphosphatase, type I, from Stenotrophomonas maltophilia K279a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NUY pdb entry 1nuy as per Morda
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 287 Rigaku Reagents JCSG+ screen, condition h12: 45% (V/V) MPD, 200mM Ammonium acetate, 100mM HEPES free acid / NaOH pH 7.5: StmaA.17936.a.B1.PW38784 at 22.75mg/ml + 4mM fructose-1,6-bisphosphate: tray: 315242h12, cryo: direct: puck: uog3-7
Crystal Properties Matthews coefficient Solvent content 2.54 51.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.04 α = 90 b = 125.73 β = 90 c = 158.45 γ = 90
Symmetry Space Group P 21 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 CCD RAYONIX MX-300 Beryllium Lenses 2018-07-23 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 2.2 50 99.7 0.078 0.084 0.999 12.72 7.359 77671 40.704
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 2.2 2.26 99.7 0.551 0.592 0.971 3.45 7.474
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 1nuy as per Morda 2.2 37.78 1.34 76881 1973 98.82 0.2145 0.2135 0.214 0.251 0.2503 0 41.87
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 12.9353 f_angle_d 0.8813 f_chiral_restr 0.051 f_plane_restr 0.0083 f_bond_d 0.0073
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9714 Nucleic Acid Atoms Solvent Atoms 465 Heterogen Atoms 20
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing PHENIX model building Coot model building