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Structure of SuhB: Inositol monophosphatase and extragenic suppressor from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Model constructed from the consensus sequences of human, MJ0109 and AF2372 enzymes
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 298 20% PEG 3350, 0.2M ammonium acetate, 0.05M TRIS, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.05 39.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.767 α = 90 b = 45.447 β = 125.43 c = 71.758 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 110 IMAGE PLATE RIGAKU RAXIS HTC Osmic blue confocal 2006-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ DW 1.5418
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 1.82 47 95 0.05 19.9 3.3 15955 15115 25
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) 1.9 1.97 36 0.27 4.1 2.6 740
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Hybrid of human and MJ IMPase 1.9 47 15113 15113 830 94.97 0.21331 0.20922 0.2027 0.28555 RANDOM 40.195
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] 0.97 -1.58 0.35 -3.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.111 r_dihedral_angle_4_deg 17.369 r_dihedral_angle_3_deg 16.895 r_dihedral_angle_1_deg 7.449 r_scangle_it 4.234 r_scbond_it 2.784 r_mcangle_it 2.087 r_angle_refined_deg 1.851 r_mcbond_it 1.288 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.111 r_dihedral_angle_4_deg 17.369 r_dihedral_angle_3_deg 16.895 r_dihedral_angle_1_deg 7.449 r_scangle_it 4.234 r_scbond_it 2.784 r_mcangle_it 2.087 r_angle_refined_deg 1.851 r_mcbond_it 1.288 r_nbtor_refined 0.314 r_nbd_refined 0.237 r_symmetry_vdw_refined 0.237 r_symmetry_hbond_refined 0.231 r_xyhbond_nbd_refined 0.192 r_chiral_restr 0.138 r_bond_refined_d 0.021 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2007 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing