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Structure of human IMP dehydrogenase, isoform 2, bound to GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Z87
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 25% (w/v) PEG-1500
0.1 M Buffer MIB (malonic acid, imadazole, boric acid), pH 9.0
Crystal Properties Matthews coefficient Solvent content 3.26 62.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.119 α = 90 b = 134.119 β = 90 c = 325.703 γ = 90
Symmetry Space Group I 4 2 2
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 2015-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.99987 Diamond I03
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 2.623 81.953 92.6 0.142 0.155 0.06 0.997 10.6 6.5 44889
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 2.623 2.827 47 1.564 1.689 0.635 0.408 1.5 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 4Z87 2.623 81.953 1.35 36415 1844 81.07 0.2206 0.2193 0.2329 0.2437 0.2521
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 14.245 f_angle_d 0.615 f_chiral_restr 0.043 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6340 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 322
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHASER phasing