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Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 293 0.2 M AMMONIUM SULPHATE, 25 % PEG3350, 0.1 M BISTRIS, PH 5.5, 20 DEG C
Crystal Properties Matthews coefficient Solvent content 2.2 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.62 α = 90 b = 105.45 β = 90 c = 263.05 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 1.75 40 99.6 0.07 11.6 4 169966 4.1
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 1.75 1.87 98.9 0.3 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.75 30 167734 2208 100 0.174 0.174 0.198 RANDOM 15.04
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] -0.61 0.27 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.221 r_scangle_it 3.331 r_scbond_it 2.102 r_mcangle_it 1.515 r_angle_refined_deg 1.218 r_mcbond_it 0.988 r_symmetry_vdw_refined 0.466 r_symmetry_hbond_refined 0.286 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.221 r_scangle_it 3.331 r_scbond_it 2.102 r_mcangle_it 1.515 r_angle_refined_deg 1.218 r_mcbond_it 0.988 r_symmetry_vdw_refined 0.466 r_symmetry_hbond_refined 0.286 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.097 r_bond_refined_d 0.008 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12408 Nucleic Acid Atoms Solvent Atoms 922 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SOLVE phasing