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Crystal structure of M. smegmatis GMP reductase with XMP* intermidiate in complex with NADP+ and IMP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other NA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 291 0.03 M Magnesium chloride
0.03 M Calcium chloride
20% (v/v) Ethylene glycol
8.5% (v/v) PEG 8000
0.1 M Tris/BICINE, pH 8.3
Crystal Properties Matthews coefficient Solvent content 2.87 57.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 204.8 α = 90 b = 204.91 β = 102.306 c = 116.15 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 16M 2024-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97625 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.1 42.55 99.3 0.1688 0.1995 0.1052 0.979 3.7 3.5 533989 45.85
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 2.1 2.12 99.07 2.21 2.596 1.349 0.171 0.61 3.7
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 2.1 42.55 1.34 269401 13469 99.3 0.22 0.2185 0.2184 0.2485 0.248 50.59
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 14.9942 f_angle_d 0.5242 f_chiral_restr 0.0418 f_plane_restr 0.0054 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27384 Nucleic Acid Atoms Solvent Atoms 741 Heterogen Atoms 752
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing Coot model building PHENIX refinement