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Structure of the IMP dehydrogenase related protein GUAB3 from Synechocystis PCC 6803
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QR6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 Crystals were grown in the presence of XMP and NAD+ in mother liquor from the condition 1-10 of the commercial screen Morpheus (Molecular Dimensions), which consists of a salt mixture (0.03M Magnesium chloride hexahydrate and 0.03M Calcium chloride dihydrate), a precipitant mix (20% v/v Ethylene glycol and 10 % w/v PEG 8000), and 0.1M of a buffer system (Tris-base, Bicine) adjusted at pH 8.5.
Initial concentrations:
Protein = 12.5 mg/mL
XMP = 3 mM
NAD = 3 mM
Crystal Properties Matthews coefficient Solvent content 2.3 46.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.98 α = 90 b = 131.68 β = 90 c = 182.495 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 PIXEL DECTRIS PILATUS 6M 2022-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979263470491 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.88 49.04 90.4 0.073 0.999 14.21 4.6 219243 31.06
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.93 35.3 0.806 0.55 0.67 1.18
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.88 49.04 1.34 219173 11046 90.4 0.1793 0.1784 0.1786 0.1967 0.1964 34.88
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 11.7327 f_angle_d 0.684 f_chiral_restr 0.0502 f_plane_restr 0.0054 f_bond_d 0.0048
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22122 Nucleic Acid Atoms Solvent Atoms 1606 Heterogen Atoms 376
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing