☰ Navigation Tabs
Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae, deletion mutant, complexed with IMP and mycophenolic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FF0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 15% tacsimate, 0.1 M Hepes buffer, 2% PEG 3350, 0.01 M IMP, 0.01 M mycophenolic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.27 45.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.909 α = 90 b = 120.909 β = 90 c = 94.871 γ = 90
Symmetry Space Group P 4 21 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 CCD ADSC QUANTUM 315r 2012-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.03 35.5 99.5 0.084 9.1 9.2 45602 45602
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.07 97.3 0.802 2.37 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4FF0 2.03 35.6 45572 43280 2292 99.38 0.16753 0.16518 0.1704 0.21337 0.2176 RANDOM 29.043
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] -1.49 -1.49 2.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.971 r_dihedral_angle_4_deg 22.27 r_dihedral_angle_3_deg 14.258 r_dihedral_angle_1_deg 6.01 r_angle_refined_deg 1.799 r_angle_other_deg 0.99 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.971 r_dihedral_angle_4_deg 22.27 r_dihedral_angle_3_deg 14.258 r_dihedral_angle_1_deg 6.01 r_angle_refined_deg 1.799 r_angle_other_deg 0.99 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5067 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 94
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing HKL-3000 phasing