☰ Navigation Tabs
Structure of human IMP dehydrogenase, isoform 2, bound to GDP
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 0.1 M sodium citrate, pH 5.5
0.2 M lithium sulphate
15% (v/v) ethanol
Crystal Properties Matthews coefficient Solvent content 3.27 62.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.729 α = 90 b = 134.729 β = 90 c = 324.081 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 PILATUS3 S 6M 2015-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.99990 ALBA XALOC
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 2.567 162 94.9 0.194 0.198 0.039 0.997 14.6 25.8 48045
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 2.567 2.753 64.2 2.617 2.696 0.517 0.629 1.6 27.1
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 2.567 162 1.35 39034 1967 81.23 0.2203 0.2187 0.2282 0.2487 0.2522
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 13.61 f_angle_d 0.657 f_chiral_restr 0.044 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6430 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 266
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHASER phasing