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Crystal structure of a human p14.5, a translational inhibitor reveals different mode of ligand binding near the invariant residues of the Yjgf/UK114 protein family
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 Sodium malonate, sodium benzoate, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.67 53.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.158 α = 90 b = 154.158 β = 90 c = 104.559 γ = 120
Symmetry Space Group P 31 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 100 IMAGE PLATE MARRESEARCH MIRRORS 2002-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 20 98.4 0.081 0.081 22.9 6.8 110385 29.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.92 94.4 0.55 0.55 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.9 20 110333 104822 5511 98.2 0.185 0.1885 0.216 0.2193 RANDOM 20.6
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] -1.24 -0.62 -1.24 1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.46 r_dihedral_angle_1_deg 15.097 r_scangle_it 3.692 r_scbond_it 2.24 r_mcangle_it 1.627 r_angle_refined_deg 1.542 r_angle_other_deg 1.467 r_mcbond_it 0.915 r_nbtor_other 0.316 r_nbd_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.46 r_dihedral_angle_1_deg 15.097 r_scangle_it 3.692 r_scbond_it 2.24 r_mcangle_it 1.627 r_angle_refined_deg 1.542 r_angle_other_deg 1.467 r_mcbond_it 0.915 r_nbtor_other 0.316 r_nbd_refined 0.298 r_symmetry_vdw_other 0.242 r_nbd_other 0.218 r_symmetry_hbond_refined 0.21 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.159 r_xyhbond_nbd_other 0.121 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8981 Nucleic Acid Atoms Solvent Atoms 443 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling SnB phasing SOLVE phasing