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Structural studies of human inositol monophosphatase-1 inhibition by ebselen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AS4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292.15 0.2 M magnesium formate and 20% (wt/vol) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.24 39.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.29 α = 90 b = 75.72 β = 95.6 c = 57.51 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315 2013-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.6 45.04 98.75 0.993 8.57 1.8 14825
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.693 0.733
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4AS4 2.6 45.04 14825 764 98.78 0.23 0.2006 0.2161 0.2436 0.2587 37.693
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] 1.162 -2.299 0.626 -1.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.411 r_dihedral_angle_3_deg 15.181 r_dihedral_angle_4_deg 12.867 r_dihedral_angle_1_deg 5.012 r_lrange_it 4.222 r_lrange_other 4.168 r_mcangle_other 2.78 r_mcangle_it 2.763 r_scangle_other 2.695 r_scangle_it 2.684
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.411 r_dihedral_angle_3_deg 15.181 r_dihedral_angle_4_deg 12.867 r_dihedral_angle_1_deg 5.012 r_lrange_it 4.222 r_lrange_other 4.168 r_mcangle_other 2.78 r_mcangle_it 2.763 r_scangle_other 2.695 r_scangle_it 2.684 r_angle_other_deg 1.893 r_scbond_other 1.743 r_mcbond_other 1.714 r_scbond_it 1.703 r_mcbond_it 1.679 r_angle_refined_deg 1.169 r_symmetry_xyhbond_nbd_refined 0.379 r_xyhbond_nbd_refined 0.294 r_nbd_other 0.242 r_symmetry_nbd_other 0.201 r_nbd_refined 0.186 r_nbtor_refined 0.178 r_symmetry_nbd_refined 0.158 r_symmetry_nbtor_other 0.092 r_symmetry_xyhbond_nbd_other 0.073 r_chiral_restr 0.06 r_bond_other_d 0.055 r_dihedral_angle_other_3_deg 0.034 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3707 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing