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Room-temperature structure of Pedobacter heparinus N-acetylglucosamine 2-epimerase at atmospheric pressure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GZ6 2GZ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 12.6 mg/ml protein in 20 mM sodium phosphate buffer pH 7.5 were mixed (4+2 ul) with 0.1 M sodium cacodylate buffer pH 5.0, 0.35 M sodium acetate and 26% PEG 8000. Crystals grew at room temperature in 5-7 days.
Crystal Properties Matthews coefficient Solvent content 2.22 44.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.945 α = 90 b = 94.626 β = 102.53 c = 82.465 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 PIXEL DECTRIS PILATUS3 X CdTe 2M 2020-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.477 PETRA III, DESY P11
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 1.5 17.62 99.67 0.176 0.1914 0.07439 0.994 5.83 6.8 135935 20.38
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 1.5 1.554 99.29 1.755 1.905 0.7352 0.495 0.89 6.7
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2GZ6 1.5 17.62 1.35 135845 1306 99.82 0.1537 0.1536 0.1589 0.1637 0.1703 29.27
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 25.6921 f_angle_d 1.043 f_chiral_restr 0.0535 f_bond_d 0.0083 f_plane_restr 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6417 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XSCALE data scaling PHENIX phasing